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383
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Lecture: "CryoEM: model building and validation" by Genki Terashi & Daisuke Kihara, the annual CCP4/APS crystallography workshops, virtual, November 4, 2024
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382
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Plenary talk, XXXIV National Congress of Biochemistry, the Mexican Biochemistry Society, Mazatlán, Mexico, October 20-25, 2024
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link
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381
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Rosen Center for Advanced Computing (RCAC) Cyberinfrastructure Symposium, Purdue University, October 22, 2024
- "Kiharalab EMSuite Server for Structure Modeling, Validation and Refinement of Cryo-EM Maps", (poster), by Han Zhu et al.
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380
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"Structure modeling and validation tools for cryo-EM", webinar, Duke University, October 8, 1pm, 2024
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379
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Workshop: "Alphafold3 & Kihara Lab Computational Tools" by Pranav Punuru, Zicong Zhang, and Daisuke Kihara, SBBC Workshop Series, Purdue University, September 24, 2024
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378
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"AI-based molecular modeling for rational drug design from cryo-EM", Purdue Institute for Drug Discovery 9th Annual Symposium, Purdue University, September 20, 2024
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377
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Biological Sciences 2024 Research Retreat, Purdue University, West Lafayette, IN, September 6-7, 2024
- "AI-based structural biology", (talk), Daisuke Kihara
- "Assessment of the Protein Function Prediction Method (PFP) by Linear Regression, Random Forest and Multilayer Perceptron", (poster), Emilia Tugolukova
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376
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Seminar: "Structure modeling using DeepMainmast and DAQ" by Tsukasa Nakamura, Osaka University, Osaka, Japan, September 5-6, 2024
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375
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Invited talk, "Biomolecular structure prediction beyond Alphafold: RNA and peptide-protein complex", Shenzhen Bay Laboratory, Shenzhen, China, August 9, 2024
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374
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Invited talk, 2024 Kuo Symposium on cryo-EM, Southern University of Science and Technology, Shenzhen, China, August 9-14, 2024
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link
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373
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Structural and Computational Biology and Biophysics Grad Student and Postdoc Symposium, Purdue University, West Lafayette, IN, July 26, 2024
- "Easy & Accurate Structure Modeling and Validation for Cryo-EM Using Web Server", Javad Baghirov
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372
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Presentation at Summer Undergraduate Research Symposium, Purdue University, West Lafayette, IN, July 25, 2024
- "Protein Structure Modeling using Deep-Learning", Anouka Saha
- "VIPER: An AI-Powered Conversational Interface for Integrated Protein Research and Structure Prediction", Pranav Punuru
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link
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371
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Webinar on web-based tools for cryo-EM structure modeling and validation, Daisuke Kihara & Genki Terashi, Hokkaido University, July 24, 2024
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370
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Advances in Structural Biology: Current Practices and Future Needs for AI Tools, organizer, Purdue University, West Lafayette, IN, July 16, 2024
- "DiffModeler and DMcloud: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using a Conditional Diffusion Model and Point Cloud Matching", Genki Terashi
- "Web-based tools for cryo-EM structure modeling and validation", Daisuke Kihara
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369
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Webinar: Achieving High-Resolution Cryo-EM Structures - From Sample Preparation to Atomic Modeling, Microscopy Society of America, July 11-12 2pm ET, 2024
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link
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368
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Invited talk, Bridging Gaps Between Cell, Structural and Computational Biology, Gordon Conference, Barcelona Spain, June 23-26, 2024
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link
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367
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Computational biomolecular structure modeling beyond Alphafold, Institute for Protein Research, Osaka University, Japan, June 14, 2024
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366
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Invited talk, The 24th Annual Meeting of the Protein Science Society of Japan, Sapporo, Japan, June 11-13, 2024
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link
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365
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Workshop: Easy and accurate structure modeling and validation on web server for cryo-EM, at 9th Annual Hitchhiker's Guide to the Biomolecular Galaxy 2024, Purdue University, May 23-24, 2024
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link
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364
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Presentation at Merck-Purdue Symposium, Purdue University, May 8, 2024
- "Peptide Docking with Privileged Knowledge Distillation using Deep Learning", (poster), Zicong Zhang
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363
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Presentation at Research in Computational Molecular Biology(RECOMB), Cambridge, MA, USA, April 29 - May 2, 2024
- "DeepMainmast: Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction", Genki Terashi, Xiao Wang, Devashish Prasad, Tsukasa Nakamura, & Daisuke Kihara
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link
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362
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Presentation at Midwest Conference on Protein Folding, Assembly, and Molecular Motions, University of Notre Dame, IN, April 27, 2024
- "Peptide Docking with Privileged Knowledge Distillation using Deep Learning", (poster), Zicong Zhang
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link
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361
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Biophysics seminar, Department of Physics, Purdue University, April 16, 2024, 1:30PM in PHYS 242
- "Computational biomolecular structure modeling beyond Alphafold", Daisuke Kihara
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360
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Frontiers in Biophysics seminar series, Department of Biological Sciences and Molecular Biophysics Training Program, Purdue University, April 10, 2024, 1:30PM in MJIS 1001
- "AlphaFold Model Confidence Score Improvement Via Deep Graph Learning", Jacob Verburgt
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359
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NuFold: RNA Structure Prediction Method Using Deep Learning with Flexible Nucleobase Center Representation, Webinar at RNA CASP Special Interest Group, April 9, 2024
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link
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358
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Invited talk: Multimodal Structure Determination using DeepMainmast and Cryo-electron Microscopy Maps, GLP - 1R Workshop, Thermo Fisher Scientific, Shanghai NNP and Online, March 19, 2024
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357
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Invited talk: Protein and DNA/RNA Structure Modeling and validation for Cryo-EM Using Deep Learning, 5th International Symposium on Cryo-3D Image Analysis 2024, Lake Tahoe, CA, March 13-16, 2024
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link
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356
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Invited talk: AI-driven 3D Structure Modeling Methods for Cryo-electron Microscopy Maps, AIST Artificial Intelligence Research Center International Symposium 2024, Tokyo, Japan, March 9-10, 2024
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link
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355
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Integrated Pipeline for Protein Docking with Extended and Enhanced Alphafold-Based Modeling Methods, 8th CAPRI Assessment Meeting, February 14-16, 2024
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link
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354
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Building Protein and DNA/RNA Structure Models from medium to low resolution cryo-EM Maps, EMBL Grenoble, France, February 14, 2024
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353
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Poster presentations at 68th Biophysical Society Annual Meeting, Philadelphia, PA, February 10-14, 2024
- "DAQ-Score Database and DAQ-refine: Deep-learning Based Quality Estimation and Refinement of Cryo-EM Derived Protein Models.", Tsukasa Nakamura
- "DeepMainmast and CryoREAD: Protein and DNA/RNA Structure Modeling for Cryo-EM Using Deep Learning.", Genki Terashi
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link
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352
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Presentation at Machine learning for protein engineering seminar, February 6, 2024
- "Domain-PFP allows protein function prediction using function-aware domain embedding representations", Nabil Ibtehaz
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link
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351
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Protein and DNA/RNA structure modeling and validation for cryo-EM, Daisuke Kihara, Genki Terashi, Xiao Wang, 2024 Cryo-EM and Cryo-VR augmented workshop, University of Jos, Nigeria, January 12, 2024
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350
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Biomolecular structure modeling for cryo-EM using deep learning, Seminar at the Cincinnati Children's Division of Biomedical Informatics, Cincinnati, OH, October 6, 2023
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349
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Online seminar at Seoul National University, Seoul, South Korea, September 21, 2023
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348
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Presentation at Purdue RCAC Advanced Computing's Cyberinfrastructure Symposium, Purdue University, Sep 12, 2023
- "CryoREAD: De novo structure modeling for DNA/RNA in cryo-EM maps using deep learning", Xiao Wang
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347
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Seminar at Mohamed bin Zayed University of Artificial Intelligence (MBZUAI), Abu Dhabi, United Arab Emirates. September 11, 2023
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346
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Invited talk: Validating and Building Biomolecular Structure Models for cryo-EM Maps Using Deep Learning, Daisuke Kihara, 26th Congress and General Assembly of the International Union of Crystallography, Melbourne, Australia, August 22-29, 2023
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link
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345
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Presentation at ACS Fall 2023, San Francisco, CA, August 13-17, 2023
- Invited talk: "Protein complex structure modeling from Cryo-EM map using deep learning", Daisuke Kihara
- "Investigating Dec-based Linker Proteins to Mediate Assembly of P22 Virus-Like Particles (VLPs)", Paulina Medina, Risako Fukazawa, Amalia Lopez, Genki Terashi, Daisuke Kihara, & Masaki Uchida
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link
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344
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Structural and Computational Biology and Biophysics Grad Student and Postdoc Symposium, Purdue University, West Lafayette, IN, July 31, 2023
- "DAQ-Score Database: Deep-learning Based Quality Estimation of Cryo-EM Derived Protein Models", Tsukasa Nakamura, Xiao Wang, Genki Terashi, & Daisuke Kihara
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343
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Webinar: Automation of Cryo-EM Workflows, July 26, 2023, 10am ET
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link
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342
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Invited talk at Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules (Virtual Only), July 24-28, 2023
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link
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341
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Poster presentation at the 37th Annual Symposium of the Protein Society, Boston, MA. United States, July 13-16, 2023
- "DAQ-Score Database: Deep-learning Based Quality Estimation of Cryo-EM Derived Protein Models", Tsukasa Nakamura, Xiao Wang, Genki Terashi, & Daisuke Kihara
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link
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340
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Oral presentation at the 73rd annual meeting of the American Crystallographic Association, Baltimore, MD, July 7-11, 2023
- "Quality Assessment and Biomolecular Structure Modeling for Cryo-EM using Deep Learning", Genki Terashi, Xiao Wang, Tsukasa Nakamura, Devashish Prasad, & Daisuke Kihara
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link
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339
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Building and Validating Biomolecular Structure Models for cryo-EM Maps Using Deep Learning, Daisuke Kihara, Seminar at The University of Tokyo, Department of Cell Biology & Anatomy, Tokyo, Japan, July 11, 2023
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338
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Building and Validating Biomolecular Structure Models for cryo-EM Maps Using Deep Learning, Daisuke Kihara, Seminar at Tokyo Institute of Technology, Tokyo, Japan, July 10, 2023
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337
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Building and Validating Biomolecular Structure Models for cryo-EM Maps Using Deep Learning, Daisuke Kihara, Seminar at Institute for Protein Research, Osaka University, Osaka, Japan, June 30, 2023
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336
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Building and Validating Biomolecular Structure Models for cryo-EM Maps Using Deep Learning, Daisuke Kihara, Seminar at Institute for Chemical Research, Kyoto University, Kyoto, Japan, June 28, 2023
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335
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Presentation at XVI Plant Cell Wall Meeting, Málaga, Spain, June 18-22, 2023
- "Amino acids essential for assembly of cellulose synthase complexes", Anna T. Olek, ... Daisuke Kihara, ..., Zicong Zhang, ..., Nicholas C. Carpita
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link
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334
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Invited talk: at Gordon Research Conference on Three Dimensional Electron Microscopy, Newry, ME, United States, June 11-16, 2023
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link
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333
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Invited talk at Modeling of Protein Interactions (MPI) 2023, Lawrence, KS, May 25-27, 2023
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link
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332
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Presentations at the Hitchhiker's Guide to the Biomolecular Galaxy Symposium, Purdue University, May 16-17, 2023
- "DeepMainmast: Protein Structure Modeling for Cryo-EM Using Deep Learning" (oral), Genki Terashi
- "De novo structure modeling for nucleic acids in cryo-EM maps using deep learning" (oral), Xiao Wang
- Workshop on "Computational Protein, DNA/RNA Structure Modeling for cryo-EM", Zicong Zhang, Charles Christoffer, Xiao Wang, Genki Terashi, & Daisuke Kihara
- "De novo structure modeling for nucleic acids in cryo-EM maps using deep learning" (poster), Xiao Wang
- "GO2SUM: Generating Human readable functional summary from GO terms" (poster), Swagarika J Giri
- "DeepMainmast: Protein Structure Modeling for Cryo-EM Using Deep Learning" (poster), Genki Terashi
- "Flex-LZerD: Protein Docking with Extremely Large Conformational Changes" (poster), Charles Christoffer
- "Distance-AF: Flexible protein structure prediction with distance constraints using AlphaFold2" (poster), Yuanyuan Zhang
- "DAQ-Score Database: Deep-learning Based Quality Estimation of Cryo-EM Derived Protein Models" (poster), Tsukasa Nakamura
- "Computational tools for protein and DNA/RNA 3D structure modeling for Cryo-EM maps" (poster), Devashish Prasad
- "NuFold: Development of RNA Tertiary Structure Prediction Method Using Machine Learning" (poster), Yuki Kagaya
- "Biomolecular structure modeling in CASP15 competition" (poster), Anika Jain
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link
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331
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Poster presentation at Midwest Conference on Protein Folding, Assembly and Molecular Motions, Notre Dame, IN, April 29, 2023
- "De novo structure modeling for nucleic acids in cryo-EM maps using deep learning", Xiao Wang
- "Flex-LZerD: Protein Docking with Extremely Large Conformational Changes", Charles Christoffer
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link
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330
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Invited talk at The 7th U.S.-Japan Digital Innovation Hub and Advanced Technology Workshop, Takasaki, Gunma, Japan, April 29, 2023
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329
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Poster presentations at ACS Spring 2023, Indianapolis, IN, March 26-30, 2023
- "DAQ-score database: Deep-learning based quality estimation of cryo-EM derived protein models.", Tsukasa Nakamura
- "deepMainmast: De novo protein structure modeling for cryo-EM with deep learning and structure prediction.", Genki Terashi
- "De novo structure modeling for nucleic acids in cryo-EM maps using deep learning.", Wang Xiao
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link
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328
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Impact of AI on Biology Research, the College of Science's Honorary Invited Lecturer Series, Purdue Fort Wayne, March 21, 2023
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link
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327
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Poster presentations at 67th Biophysical Society Annual Meeting, San Diego, CA, February 18-22, 2023
- "Flex-LZerD: Protein Docking with Extremely Large Conformational Changes." (poster), Charles Christoffer
- "DAQ-Score Database: Deep-learning Based Quality Estimation of Cryo-EM Derived Protein Models." (poster), Tsukasa Nakamura
- "DAQ-refine: Protein Structure Model Evaluation and Refinement for Cryo-EM." (poster), Genki Terashi
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link
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326
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Invited talk: at Biophysics and Quantitative Biology in the AI Era, Carnegie Mellon University, PA, United States, January 12-13, 2023
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link
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325
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One World Cryo-EM online seminar, October 5, 2022
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link
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324
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Genki Terashi, "Protein Structure Modeling and Quality Evaluation from Cryo-EM maps Using DAQ Score", RIKEN, Japan, October 5, 2022
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323
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Genki Terashi, "Protein Structure Modeling and Quality Evaluation from Cryo-EM maps Using DAQ Score", Department of Biological Sciences, Chuo University, Japan, October 3, 2022
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link
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322
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2nd Princeton-Nature Conference: Frontiers in Electron Microscopy for the Physical and Life Sciences, Princeton University, NJ, September 28-30, 2022
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link
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321
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Invited talk, Workshop on Machine Learning in cryo-EM, National University of Singapore, September 19-23, 2022
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link
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320
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Genki Terashi, "Machine-Learning Based Local Quality Estimation for Protein Structure Models from cryo-EM Maps", at Informatics in Biology, Medicine and Pharmacology (IIBMP) Osaka, Japan, Sep. 13-15, 2022
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link
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319
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Genki Terashi, "Residue-wise local quality estimation for protein models from cryo-EM maps", Osaka University, Japan, September 12, 2022
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318
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Invited talk, Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules, Telluride CO, July 25-29, 2022
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317
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Eman Alnabati, PhD thesis defense, "Protein Structural Modeling Using Electron Microscopy Maps", Purdue University, July 14, 2022
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316
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"Protein structure modeling and model quality assessment for cryo-EM density maps using deep learning", Nagoya University, July 6, 2022
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315
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"Protein structure modeling and model quality assessment for cryo-EM density maps using deep learning", Structural Biology Research Center International Cryo-EM Seminar Series, High Energy Accelerator Research Organization KEK, Tsukuba, Japan, July 1, 2022
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314
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Invited talk, "Deep Learning Applications to Protein Modeling and Quality Assessment for Cryo-Electron Microscopy", 6th International Conference on Mathematical and Computational Medicine, Telluride CO, June 11-15, 2022
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313
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ODSS Software Tools for Open Science 2022, NIH, virtual meeting, June 2-3, 2022
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312
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Sai Raghavendra Maddhuri Venkata Subramaniya, PhD thesis defense,"Deep learning enabled 3D protein structure modeling", Purdue University, May 16, 2022
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311
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Presentations at the Hitchhiker's Guide to the Biomolecular Galaxy Symposium, Purdue University, May 11-12, 2022
- "Real-time structure search and structure classification for Alphafold protein models" (oral), Tunde Aderinwale
- "Modeling of GPCR complexes in GPCR-Dock 2021" (poster), Jacob Verburgt
- Workshop on "Insights into Alphafold", D. Kihara & Zicong Zhang
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310
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2 Presentations at the Midwest Protein Folding Symposium, University of Notre Dame, Indiana, May 7, 2022
- "Real-time structure search and structure classification for Alphafold protein models" (oral and poster), Tunde Aderinwale
- "Modeling of GPCR complexes in GPCR-Dock 2021" (poster), Jacob Verburgt
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309
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Lyman Monroe, PhD thesis defense, "Molecular dynamics in protein structure quality assessment and refinement", Purdue University, April 6, 2022
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308
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Invited talk, "Protein 3D structure modeling from medium-resolution cryo-EM density maps", at the 4th International Symposium on Cryo-3D Image Analysis 2022, Lake Tahoe, March 9-12, 2022
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link
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307
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"Deep learning-based local quality estimation for protein structure models from cyro-EM maps" (poster), 66th Biophysical Society Annual Meeting, San Francisco, Feb. 19-23, 2022
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306
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Invited talk "Protein 3D structure modeling from medium-resolution cryo-EM density maps" at Pacifichem 2021 , Honolulu, Hawaii December 16-17, 2021
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link
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305
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"Cryo-EM flexible fitting refinement with automatic error fixing for de novo protein structure modeling" (poster), Takaharu Mori, G. Terashi, D. Matsuoka, D. Kihara, Y. Sugita, The 59th Annual Meeting of The Biophysical Society of Japan, Sendai, Japan, Nov. 25-27, 2021
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304
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Talk by Genki Terashi, The 49th QSAR Symposium, The Pharmaceutical Society of Japan (virtual conference), Nov 18-19, 2021
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303
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"Drug development and beyond: Protein-protein interaction (PPI) drugs and deep-learning assisted computational protein docking", College of Pharmacy & Health Sciences, Butler University, Nov 18, 2021
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302
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"Computational protein docking modeling with application of deep learning", Vellore Institute of Technology (VIT), India, Nov. 17, 2021
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301
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"Deep learning-assisted protein 3D structure modeling for medium resolution cryo-EM density maps", Dept. of Computer Science, University of Central Florida, November 9, 2021
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300
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"Volume segmentation and vector-based map alignment for cryo-EM maps", invited talk by Genki Terashi, X. Han, C. Christoffer, & D. Kihara, 3rd IEEE International Conference on BioInspired Processing, BIP 2021, Costa Rica (virtual conference), Nov 4-5, 2021
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299
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"Deep learning-assisted protein 3D structure modeling for medium resolution cryo-EM density maps", Rossmann Symposium, Purdue University, Oct. 25, 2021
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298
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"Deep learning-assisted protein 3D structure modeling for medium resolution cryo-EM density maps", EMBO Workshop: Advances and Challenges in Biomolecular Simulations, (virtual conference), Oct. 18-21, 2021
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297
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"Deep learning-assisted protein 3D structure modeling for medium resolution cryo-EM density maps", Invited talk at University of Washington, Seattle,Oct. 12 , 2021
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296
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"The OC_Finder: A deep learning-based software for in vitro osteoclast counting", Mizuho Kittaka, Xiao Wang, Yilin He, Yiwei Zhang, Daisuke Kihara, Yasuyoshi Ueki, 2021 Annual Meeting of The American Society for Bone and Mineral Research, October 1-4, 2021
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295
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Invited talk "Protein structural bioinformatics after CASP14" at Informatics in Biology, Medicine and Pharmacology (IIBMP) Tokyo, Japan, Sep. 27-29, 2021
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294
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Lecture "Machine learning in protein structure bioinformatics" at the 2nd Summer School on Machine Learning in Bioinformatics (online), HSE University, Moscow, Russia, Aug 23-27, 2021
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293
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Keynote talk "Deep-learning-assisted protein 3D struture modeling for medium-resolution cryo-EM density maps", D. Kihara, BIOKDD 2021 , Aug 15, 2021
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link
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292
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2 oral presentations at the 71st Annual Meeting of the American Crystallographic Association, July 30 - Aug. 5, 2021
- "Emap2sec+: Decting protein and DNA/RNA stru tures in cryo-EM maps of intermediate resolution using deep learning." Xiao Wang, E. Alnabati, TW Aderinwale, SR Maddhuri Venkata Subramaniya, G. Terashi, D. Kihara
- "MAINMAST: De novo protein structure modeling for cryo-EM maps assisted by structrure feature detection by deep learning". Genki Terashi, X. Wang, D. Kihara
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291
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"Deep-learning-assisted protein 3D structure modeling for medium-resolution croy-EM density maps", D. Kihara, 5th International Conference on Mathematical and Computational Medicine, (Virtual meeting), June 7-11, 2021
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290
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"Efficient flexible fitting refinement for de novo structure modeling from cryo-EM density maps" (poster). Takaharu Mori, G. Terashi, D. Matsuoka, D. Kihara, Y. Sugita. The 21st Annual Meeting of the Protein Science Society of Japan, Tsukuba, Japan, June 7-9, 2021
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289
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3 oral presentations at The Hitchhiker's Guide to the Biomolecular Galaxy 2021, May 12-13, 2021
- "VESPER: Global and local cryo-EM map alignment and database search using local density vectors", Genki Terashi et al.
- "Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning", Xiao Wang et al.
- "Modeling transmembrane protein interactions using topological and biophysical principles", Daipayan Sarkar et al.
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link
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288
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1 oral and 2 poster presentations at 2021 65th Biophysical Society Annual Meeting, February 22-26, 2021
- (oral) Super resolution cryo-EM maps with 3D generative adversarial networks. Sai Raghavendra Madhuri Venkata Subramaniya, Genki Terashi, & D. Kihara
- Emap2sec+: Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning. Xiao Wang, Eman Alnabati, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & D. Kihara
- VESPER:Global and local cryo-EM map alignment and database search using local density vectors. Genki Terashi, Xusi Han, Charles Christoffer, Siyang Chen, & D. Kihara
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link
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287
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3 poster presentations at Frontiers in Cryo-Electron Microscopy, Keystone Symposia, Feb. 3-4, 2021
- Emap2sec+: Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning. Xiao Wang, Eman Alnabati, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & D. Kihara
- VESPER:Global and local cryo-EM map alignment and database search using local density vectors. Genki Terashi, Xusi Han, Charles Christoffer, Siyang Chen, & D. Kihara
- Super resolution cryo-EM maps with 3D generative adversarial networks. Sai Raghavendra Madhuri Venkata Subramaniya, Genki Terashi, & D. Kihara
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286
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"Protein 3D structure modeling for medium-resolution cryo-EM density maps", Online Seminar at the CMU-Pitt CPCB Seminar series, October 30, 2020
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link
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285
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2 poster presentations at 5th Annual Southern California Cryo-EM Symposium, Oct 30, 2020
- Emap2sec+: Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning. Xiao Wang, Eman Alnabati, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & D. Kihara
- De novo protein structure modeling tool MAINMAST for multiple chain complexes, bound ligands in EM masp and map alignment. Genki Terashi, Xusi Han, Siyang Chen, Yuki Kagaya, & D. Kihara
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link
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284
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Deep learning for detecting 3D structures of biomolecules, Data Science and Machine Learning seminar series, Purdue Fort Wayne, October 6th, 2020
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283
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Oral (video) presentations at ISMB 2020, July 13-16, 2020
- EM map segmentation and de novo protein structure modeling for multiple chain complexes with MAINMAST. Genki Terashi, Y. Kagaya, & D. Kihara
- Protein contact map denoising using generative adversarial networks. Sai Raghavendra Maddhuri Venkata Subramaniya, A. Jain, Y. Kagaya, & D. Kihara
- ContactPFP: Protein function prediction using predicted contact information. Yuki Kagaya, S. Flannery, A. Jain, & D. Kihara
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link
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282
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2020 Midwest Consortium for High-resolution cryo-EM, March 5, 2020. Poster presentation: "Protein secondary structure detection in intermediate resolution cryo-EM maps using deep learning" Sai Raghavendra Maddhuri Venkata Subramanya, G. Terashi, D. Kihara
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281
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Purdue CS department, PhD Visit Day, area talk and a poster, March 2, 2020
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280
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Biophysical Society meeting,an oral and 2 poster presentations, Feb 15-19, 2020
- (talk) "De novo protein structure modeling tool MAINMAST enhanced for multiple chain complexes and bound ligands" G. Terashi, D. Kihara
- (poster) "De novo computational proteink tertiary structure modeling pipeline for cryo-EM maps of intermediate resolution" D. Kihara, G. Terashi, S.R.M.V. Subramanya
- (Poster) "Protein secondary structure detection in intermediate resolution cryo-EM maps using deep learning" Sai Raghavendra Maddhuri Venkata Subramanya, G. Terashi, D. Kihara
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279
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"Ema2sec: Protein secondary structure detection in intermediate resolution cryo-EM maps using deep learning", Sai Raghavendra Maddhuri Venkata Subramanya, Genki Terashi, D. Kihara, Workshop on "Learning Meaningful Representations of Life", 33rd Conference on Neural Information Processing Systems (NeurIPS), Vancouver, Canada, December 13, 2019
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278
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Invited talk "Protein 3D structure modeling from cryo-EM density maps", at The 5th International Conference on Protein and RNA Structure Prediction, Punta Cana, Dominican Republic, December 2-6, 2019
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277
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"Deep neural network-assisted protein structure modeling for drug development from low-resolution 3D cryo-EM maps", Annual Symposium of Purdue Institute of Drug Discovery, October 14, 2019
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276
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"Computational protein tertiary structure modeling from cryo-EM maps of intermediate resolution", D. Kihara, Dept. of Physics, Purdue University, Sep 10, 1:30pm, PHS242
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275
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invited talk (Kihara), Latin American High Performance Computing Conference (CARLA) 2019, University of Costa Rica, Sept 25-27, 2019
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274
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"Protein structure modeling for structure-based drug design", invited talk (Kihara), Symposium on Studies and development of treatment for rare disease, Ritsumeikan University, Shiga, Japan, Aug 30 2019
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273
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"Computational protein tertiary structure modeling from cryo-EM maps of intermediate resolution", Workshop on Mathematics and Computer Science in Modeling and Understanding of Structure and Dynamics of Biomolecules, Banff International Research Station for Mathematical Innovation and Discovery (BIRS), Banff, Alberta, Canada, August 9-11, 2019
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272
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"Enhancement for MAINMAST, de novo main-chain tracing method:symmetric multi-chain modeling, local refinement, and graphical user interface" (platform presentation), Genki Terashi, Yuhong Zha, & D. Kihara M&M 2019 Microscopy & Microanalysis , Portland OR, August 4-8, 2019
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link
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271
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"Defining the critical amino acids in the plant-conserved region and class-specific regions of cellulose synhase catalytic domains", Phlip Rushton, Anna T. Olek, Lee Makowski, John Badger, C. Nicklaus Steussy, Cynthia Stauffacher, Daisuke Kihara, Maureen C. McCann, Nicholas Carpita, XV Cell Wall Meeting, July 7-12 , 2019, Cambridge UK
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link
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270
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"Computational protein tertiary structure modeling from cryo-EM maps, protein docking, and protein 3D shape analysis", AIST, Tokyo, Japan, July 11, 2019
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269
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"Computational protein tertiary structure modeling from cryo-EM maps of intermediate resolution", RIKEN, Waco, Japan, July 8, 2019
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268
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"Computational protein tertiary structure modeling from cryo-EM maps of intermediate resolution", Tohoku University, Dept. of Computer Science, Sendai, Japan, July 5, 2019
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267
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Lactose derivatives as potential inhibitors of pectin methyltransferases, Melanie L'Enfant, Pricillia Kutudila, Catherine Rayon, Jean-Marc Domon, Woong-Hee Shin, Daisuke Kihara, Anne Wadouachi, Jerome Pelloux, Gwladys Pouceau, Corinne Pau-Roblot, Reseau francais des parois, May 13-16, 2019, Roscoff, France
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266
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2019 Purdue Hitchhiker's Guide to the Biomolecular Galaxy Symposium , May 8-9 , 2019
- LZerD pipeline for template-based and ab initio protein-protein interaction modeling (oral), Charles Christoffer
- Improved de novo main-chain tracing method MAINMAST for multi-chain modeling, local refinement, and graphical user interface (poster), Genki Terashi, Yuhong Zha, & D. Kihara
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link
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265
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Improved de novo main-chain tracing method MAINMAST for multi-chain modeling, local refinement, and graphical user interface (poster), Genki Terashi, Yuhong Zha, & D. Kihara, Missouri Symposium in Molecular Biophysics, Structural Electron Microscopy , April 25-26, 2019
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link
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264
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7th CAPRI Evaluation meeting, April 3-5, 2019, Hinxton,UK
- (oral) Human and LZerD server pipeline for template-based and ab initio protein-protein interaction modeling
- (poster)Extending computational protein complex modeling: Disordered protein interactions & Assembly order of multimeric protein complexes
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263
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Computational protein structure modeling for medium to low resolution cryo-electron microscopy, 16th Annual Conference of the Midsouth Computational Biology & Bioinformatics Society (MCBIOS '19), March 28-30, 2019
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link
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262
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2019 Annual Biophysical Society Meeting, Baltimore, MD, March 2-6, 2019
- Improved de novo main-chain tracing method MAINMAST for multi-chain modeling, local refinement, and graphical user interface (poster), Genki Terashi, Yuhong Zha, & D. Kihara March 6, 2857-Pos Poster Num. B529
- Modeling the assembly order of multimeric heteroprotein complexes (poster), Lenna X. Peterson et al. March 4, 964-Pos, Poster Num. B66
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link
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261
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Sigma Xi Purdue Chapter poster competition, Feb. 20 (Wed), 6-9pm, Steward 218 A-D, Purdue.
- "De novo main-chain modeling for EM maps using MAINMAST", Genki Terashi
- "Accelerating protein function discovery using computational tools",Aashish Jain
- "Emap2sec: protein secondary structure detection in intermediate resolution cryo-EM maps using deep learning", Sai Raghavendra Maddhuri Venkata Subraman
- "PL-Patchsurfer: a virtual screening program for template-based modeling structure using molecular surfaces",Woong-Hee Shin
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link
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260
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Computational prediction of protein toxicity from sequence using gene ontology terms(oral), Aashish Jain & D. Kihara, 2019 ASM Biothreats, Jan 29-31, 2019
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link
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259
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CASP13 evaluation meeting, Round table discussion on CAPRI protein docking session, Cancun, Mexico, Dec. 1-4, 2018
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link
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258
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"Identification of protein complexes in the Cyanothece ATCC51142 using proteomics and bioinformatics analysis", Ziyun Ding, Proteomics Facility Graduate Student Research Symposium, Bindley Bioscience Center, Purdue, Nov. 7, 2018, MRGN121
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257
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"Computational modeling of protein-protein interactions", Indiana University, Dept. of Chemistry, Bloomington, Oct 16 (Tue), 2018
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link
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256
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Purdue Institute for Drug Discovery, 5th Annual Symposium , Sep. 28 (Fri), Stewart Center, Purdue University 2018
- 14:55-15:00, research project presentation (D. Kihara)
- (poster) "PL-PatchSurfer2: A virtual screening method tolerant to receptor structure variation using surface patch matching", Woong-Hee Shin & D. Kihara
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link
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255
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"Computational protein structure modeling for high to medium resolution cryo-electron microscopy density maps", University of Illinois, Urbana-Champaign, 2269 Beckman Institute, Sept. 24, 2018, 3pm
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link
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254
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"Computational prediction and modeling for protein-drug and protein-protein interactions", The University of Alabama at Birmingham, Sept. 14, 2018
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253
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"De novo protein structure modeling for cryo-EM maps", Coarse-grained modeling of structure and dynamics of biomacromolecules, Telluride, CO, July 23-27, 2018
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link
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252
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3D-SIG at ISMB, Chicago, IL
- "Predicting the assembly order of multimeric heteroprotein complexes", LX Peterson, Y. Togawa, J. Esquivel-Rodriguez, G. Terashi, C. Christoffer, A. Roy, W.H Shin, D. Kihara
- "MAINMAST: De novo main-chain modeling for EM maps using tree-graph optimization." G. Terashi, D. Kihara
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link
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251
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"Computational protein structure modeling for medium to low resolution cryo-EM density maps", D. Kihara, National Institutes for Quantum and Radiological Science and Technology, Kizu, Nara, Japan, July 4, 2018
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250
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"Computational protein structure modeling for medium to low resolution cryo-EM density maps", D. Kihara, AIST, Tokyo, June 25, 2018
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249
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"Algorithm and Chimera plugin of MAINMAST, de novo main-chain tracing method for EM Maps", (talk and poster) Genki Terashi and Yuhong Zha, and D. Kihara Hitchhiker's Guide to to the Biomolecular Galaxy, May 9-10, 2018, Purdue University
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link
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248
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"Detecting multifunctional proteins by applying deep learning to academic literature", Hareesh Gali, Purdue Undergraduate Research Poster Symposium, Apr 10 (Tue), 2018, PMU Ballrooms, Purdue University
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link
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247
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62nd Biophysical Society Annual Meeting, San Francisco, CA, February 17-21, 2018
- (platform) MAINMAST: De novo main-chain model tracing for EM maps using tree-graph optimization method, Genki Terashi, & D. Kihara (2/18, 5:15pm, Rm207/208)
- (poster) Reliability of electron microscopy atomic model refinement, Lyman Monroe, G. Terashi, & D. Kihara
- (poster) Structure modeling of disordered protein interactions, L.X.Peterson, A. Roy, C. Christoffer, G. Terashi, & D. Kihara
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link
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246
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Sigma Xi Research Award Poster Competition, Stewart 218A-D, Purdue University, Feb. 21 (Wed), 2018
- Computational methods for predicting protein-protein interactions in plants, Ziyun Ding, D. Kihara
- Structure Fitting for low-resolution EM maps, Eman Alnabati, Juan Esquivel-Rodriguez, D. Kihara
- Local structure detection in cryo-EM maps, Sai Raghavendra Madduhuri, Genki Terashi, D. Kihara
- PL-PatchSurfer2: a virtual screening method tolerant to receptor structure variation using surface-patch matching, Woong-Hee Shin, D. Kihara
- Elastic network models for flexible protein-protein docking, Charles Christoffer, D. Kihara
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245
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"Computational protein structure modeling for medium to low resolution cyro-electron microscopy density maps", Daisuke Kihara, Biochemistry Seminar, Purdue University, Jan. 16, 2018
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244
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"Structure modeling of disordered protein interactions", D. Kihara, the 4th International conference on protein & RNA structure prediction, Montego Bay, Jamaica, Dec. 5-8, 2017
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243
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modeling report at CryoEM Structure Challenges Workshop, Stanford Univ., CA, Oct 6-8, 2017
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link
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242
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ISMB 2017, Prague, Czech Republic, July 21-25, 2017
- (oral)DextMP: Deep dive into text for predicting moonlighting proteins, Ishita Khan, Mansurul Bhuiyan, & D. Kihara
- 3DSIG, (Keynote): Protein bioinformatics of low-resolution structural data, D. Kihara
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link
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241
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"Computational modeling of various types of protein complexes", July 14, 2017, AIST, Tokyo, Japan
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240
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"In silico screening of biomolecules", July 12, 2017, Ono Pharmaceutical, Kyoto, Japan
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239
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"Molecular surface-based in silico screening of biomolecules", July 10, 2017, Teijin-Pharma, Tokyo, Japan
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238
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Uma Aryal, Victoria Hedrick, Tiago Sobreira, Christina Ferreira, Ziyun Ding, Daisuke Kihara, Louis Sherman, "Global analysis of native protein complexes in Cyanothecesp. ATCC 51142 using label-free quantitative proteomic profiling", Annual Conference of American Soc. for Mass Spectrometry, Indianapolis, IN, June 4-8, 2017
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237
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Daisuke Kihara, "Computational modeling of flexible protein-protein and protein-drug interactions", Computational Biophysics to Systems Biology (CBSB2017), Cincinnati, Ohio, May 18-20, 2017
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link
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236
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Great Lakes Bioinformatics Conference (GLBIO) 2017, The Univ. Illinois at Chicago, Chicago, IL, May 15-17, 2017. 4 oral/poster presentations:
- Aashish Jain & D. Kihara "Phylo-PFP: Highly accurate phylogenomics-based protein function prediction method"
- Lyman Monroe, Genki Terashi, & D. Kihara, "Variability of protein structure models from electron microscopy"
- Woong-Hee Shin, Lingfei Zhang, Xiaolei Zhu,Sung Hoon Park, Chiwook Park, W. Andy Tao, & D. Kihara "Molecular surface-based screening methods for repurposing drugs: application to find novel NAD binders in the E. coli proteome."
- Genki Terashi, D. Kihara "MAINMAST: Building main-chain models for medium resolution electron microscopy maps"
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link
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235
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Multiple presentations at The Hitchhikers' Guide to the Biomolecular Galaxy, Purdue Univerity, May 10-11 , 2017
- (oral) Aashish Jain & D. Kihara "Phylo-PFP: Highly accurate phylogenomics-based protein function prediction method"
- (oral) Lyman Monroe, Genki Terashi, & D. Kihara, "Variability of protein structure models from electron microscopy"
- (poster) Genki Terashi, D. Kihara "MAINMAST: Building main-chain models for medium resolution electron microscopy maps"
- (poster) Ziyun Ding, D. Kihara, "Computational methods for predicting protein-protein interactions in plants"
- (poster) Xusi Han, D. Kihara ,"Navigating 3D electron microscopy density maps and protein shapes with EM-SURFER and 3D-SURFER2.0"
- (poster) Sai Raghavendra Maddhuri, Genki Terashi, D. Kihara, "Structure detection in cryo-EM maps"
- (poster) Mengmeng Zhu, D. Kihara, "Efficient computational framework for biological 3D image data retrieval"
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link
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234
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Multiple poster presentations at Tessman Symposium, Purdue Univerity, May 1, 2017
- Lyman Monroe, Genki Terashi, & D. Kihara, "Variability of protein structure models from electron microscopy"
- Genki Terashi, D. Kihara "MAINMAST: Building main-chain models for medium resolution electron microscopy maps"
- Ziyun Ding, D. Kihara, "Computational methods for predicting protein-protein interactions in plants"
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link
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233
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Caleb Belth, Mengmeng Zhu, Rayan Chikhi, D. Kihara, "Using deep learning to predict binding ligands and drugs to protein targets", 2017 Undergraduate Research and Poster Symposium, Purdue University, April 11, 2017
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232
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Lenna X. Peterson, PhD Thesis defense, "Computational modeling of multifarious protein interactions", NLSN 1215, Purdue University, Apr 6, 2017
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231
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Rushton, Rayon, Olek, Makowski, Kim, Badger, Kihara, Steussy, Stauffacher, & Carpita, "Structure of the catalytic domain of a plant CesA", 253rd ACS National Meeting, April 2-6, 2017
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230
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Woong-Hee Shin, Structural Biology Seminar, Purdue University, Feb. 1 2017
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229
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"In silico screening and modeling of protein-drug and protein-protein interactions", Albert Einstein College of Medicine, New York, NY, Jan. 24 , 2017
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link
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228
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12th Critical Assessment of Techniques for Protein Structure Prediction (CASP12) Evaluation meeting, CAPRI docking & Quality assessment round table Gaeta, Italy, December 10-13, 2016
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link
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227
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Biomedical Informatics Speaker Series, Cincinnati Children's Hospital & University of Cincinnati, "In silico screening and modeling of protein-drug and protein-protein interactions", Nov. 18, 11am
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226
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Purdue University Center for Cancer Research Seminar Series, "In silico screening and modeling of protein-drug and protein-protein interactions", Purdue Institute for drug discovery lobby conference room, 11:30-12:30, November 17, 2016
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225
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D. Kihara, "Predicting gene functions: Departing from single gene-single function paradigm", Bioinformatics seminar, Purdue University, Oct. 25 (Tue), 11am-noon, 2016, at FORS 216
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link
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224
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D. Kihara, "Genome-wide discovery of protein-ligand interactions by a combined computational and energy-based approach", International Conference on Computational Genomics and Proteomics, Guanacaste, Costa Rica, Oct. 18-22, 2016
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223
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Woong-Hee Shin & D.Kihara, poster presentation and a short talk on "PL-PatchSurfer2.0: Improved local surface matching-based virtual screening method that is tolerant to target and structure variation", Drug discovery 3rd Annual Symposium, Ross Ade Pavilion, Purdue University Sep. 30, 2016
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222
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Ishita Khan, Ph.D. thesis defense, Dept. of Computer Science, LWSN building, Room 1142, Purdue University, 1pm, July 25, 2016
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221
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"The Boltzmann Sequence-Structure Channel" by A. Magner, D. Kihara, & W. Szpankowski, IEEE International Symposium in Information Theory, Barcelona, Spain, July 10-15, 2016
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link
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220
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"Ensemble-based evaluation for protein structure models" (oral presentation), ISMB, Orlando Florida,July 10-12, 2016
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link
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219
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"Considering chain flexibility in protein structure evaluation" (oral presentation), 3D-SIG, Orlando Florida,July 8-9, 2016
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link
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218
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"Genome-scale prediction of moonlighting proteins using diverse protein association information" (oral presentation), Function-SIG at ISMB, Orlando Florida,July 9, 2016
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link
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217
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"PL-PatchSurfer: Molecular surface-based virtual screening program", National Institute of Advanced Industrial and Science, Tokyo Japan, June 17, 2016
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216
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D. Kihara, Molecular modeling of energy storage devices & Biomolecular complexes, CERM 2016 47th Central Region Meeting of American Chemical Society, May 19, 2016
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link
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215
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D. Kihara, "Ensemble-based evaluation for protein structure models" The 3rd International Conference on Mathematical & Computational Medicine May 16-18, 2016
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link
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214
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The Hitchhiker's guide to the biomolecular galaxy, ARMS1010, Purdue University, May 11-12, 2016:
- (talk)"IDR-LZerD: structure prediction of disordered protein interactions", Lenna Peterson
- (talk)"An automated Calpha tracing from cryo-EM map", Genki Terashi
- (poster)"Identification of protein-protein interactions in Arabidopsis thaliana using mass spectrometry and computational methods", Ziyun Ding
- (poster) "Navigating 3D Electron Microscopy Density Maps and Protein Shapes with EM-SURFER and 3D-SURFER 2.0 ", Xusi Han
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link
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213
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D. Kihara, "Human and server prediction using LZerD with combined scoring functions", 6th CPARI protein docking prediction evaluation meeting, April 17-19 2016, Tel Aviv, Israel
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link
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212
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Josh McGraw, "Significance of amino acid entropy and mutual information in multiple sequence alignments", Undergraduate Research Poster Symposium, April 12, 2016, Purdue Memorial Union Ballroom, Purdue University
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211
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D. Kihara, "Computational docking of multifarious protein complexes", Dept. of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Feb. 29, 2016
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210
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Woong-Hee Shin, D. Kihara, "PL-PatchSurfer: A fast surface-patch-based virtual screening program using three dimensional Zernike descriptors", 60th Biophysical Society meeting , Los Angeles, Feb. 27- March 2, 2016
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link
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209
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D. Kihara, 3rd International Conference on Protein and RNA Structure Prediction, Punta Cana, Dominican Republic, Dec. 14-18, 2015
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208
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D. Kihara, "Unified biomolecular 3D surface matching for big data in structural and chemical biology", Workshop on Big Data and Computational Sciences, University of Kansas, Lawrence, Kansas, Nov. 21, 2015
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207
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D. Kihara, "Patch-Surfer and PL-PatchSurfer: Predicting binding ligands for target proteins by molecular surface similarity and complementarity", University of Kansas, Lawrence, Kansas, Nov. 20, 2015
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link
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206
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D. Kihara, The 15th KIAS Conference on Protein Structure and Function, Seoul, Korea Sept. 17-19 , 2015
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link
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205
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D. Kihara, "On the origin of protein superfamilies and superfolds", 4th SNU Bioinformatics Workshop, Seoul National University, Seoul, Korea, August 18-19, 2015
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link
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204
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D. Kihara "Origin of protein superfamiies and superfolds" (oral presentation), 3D-SIG 2015, Dublin, Ireland, July 10-11, 2015. Received the Best Oral Presentation Award
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link
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203
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D. Kihara,"Gene function prediction in biological contexts", Hokkaido University, Sapporo, Japan, July 2 , 2015
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202
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"Genome-scale identification and characterization of moonlighting proteins", I.Khan & D. Kihara, The 15th Annual Meeting of the Protein Science Society of Japan, Tokushima, Japan, June 24-26, 2015
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link
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201
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"Surface structure-based ligand prediction for target proteins and application for drug development", D. Kihara, Workshop on "Drug development based on predicted structure and function of target proteins", Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan, June 23 , 2015
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200
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"Multi-residue scoring function for selecting decoys in protein structure prediction", D. Kihara, The Chem-Bio Informatics Society, Tokyo, Japan, June 22, 2015
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link
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199
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"Comparison and fitting of molecular shapes for low-resolution structural data" D. Kihara, RIKEN, Yokohama, Japan, June 19, 2015
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198
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Great Lakes Bioinformatics Conference (GLBIO), Purdue University, West Lafayette, IN, May 18-20, 2015
- (full paper, oral presentation) "IAS: Interaction specific Go term associations for predicting protein-protein interaction networks", Satwica Yerneni, Ishita K. Khan, Qing Wei & D.Kihara
- (oral presentation) "Reissue environment score for selecting protein structure models and protein-protein docking models" Hyung-Rae Kim
- (poster) "Protein side-chain conformation prediction methods are accurate in different residue environments", Lenna Peterson, Xuejiao Kang, & D. Kihara
- (poster) "Genome scale identification and characterization of moonlighting proteins" Ishita K. Khan
- (poster) "PL-PatchSurfer2.0: A fast virtual screening program using surface patch based on 3D Zernike descriptors" Woong-Hee Shin
- (poster) "Fitting of multiple chains by iterative manipulation of Cyro-EM maps" Lyman Monroe
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link
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197
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"Detecting local residue environment similarity for recognizing near-native structure models", D.Kihara From Computational Biophysics to Systems Biology (CBSB2015), Oklahoma City, Oklahoma May 17-19, 2015
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link
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196
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A Purdue Mini-symposium on Integrated Structure, Function, and Interactions of the Protein Universe", Purdue University, IN, May 13-14, 2015
- EM-Surfer, D. Kihara
- PL-PatchSurfer, Wooong-Hee Shin
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link
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195
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Undergraduate Research and Poster Symposium, Purdue University, West Lafayette, IN, April 14, 2015
- "Distributed heterogeneous cluster computing with computational proteomics", Aditya Vaidyam, & D.Kihara
- "Analysis of bioinformatics databases", Weichuan Luo, Tiange Dong, Andrew Walden, Tianmu Hu, Ray Ji, Eric Petit, Tomii Lee, & D. Kihara
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194
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Fast shape-based global and local electron density map search (oral presentation). J. Esquivel-Rodriguez, X. Han, C. Christoffer, X. Kang, L. Monroe, & D. Kihara, the 59 th Biophysical Society Annual Meeting, Baltimore, MA, Feb. 7-11, 2015.
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link
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193
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"Phase transition in a sequence-structure channel", A. Magner, D. Kihara &. W. Szpankowski. Information Theory and Applications, Scripps Seaside Forum, La Jolla, CA, Feb. 1-3, 2015.
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link
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192
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Local image comparison using Krawtchouk moment invariants. A. Sit & D. Kihara, 2015
Joint Mathematics Meetings, San Antonio, Jan. 12, 2015
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link
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191
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Invited talk at Free Modeling category, 11th Community Wide Experiment on the Critical
Assessment of Techniques for Protein Structure Prediction (CASP11), Riviera Maya, Mexico,
Dec. 7-10, 2014
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link
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190
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"Exploring protein-ligand interactions using molecular local surface comparison methods." Dept. of Chemistry, Purdue University, Dec. 5, 2014
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189
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Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules, Telluride, CO, Aug 4-8, 2014
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link
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188
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"A proteomic strategy for global analysis of protein complex composition and localization in Arabidopsis leaves". Aryal Uma, Jun Xie, Daisuke Kihara, Mark Hall, Dan Szymanski, 25th International Conference on Arabidopsis Research (ICAR), University of British Columbia, Vancouver, Canada, July 28-Aug. 1 , 2014
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187
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"Comparison and fitting of molecular shapes and low-resolution structural data", EBI, Hinxton, UK, A2:33 (group floor EBI main building) 14:00-15:00, July 28, 2014.
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186
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"Genome-scale Identification and Characterization of Moonlighting Proteins" (selected oral presentation), The Biological and Biomedical Consequences of Protein Moonlighting , Charles Darwin House, London, UK, 29-30 July 2014
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link
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185
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"Why Protein Folds and Superfamilies have Skewed Distributions?" Zing Conference on Protein Folding, July 16-19, 2014, Punta Cana, Dominican Republic
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link
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184
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Plant Biology 2014, Portland, Oregon, Jul 12-16 , 2014.
- "Small-angle x-ray scattering reveals the structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers." P.S. Rushton, N. Carpita A.T. Olek, C.V. Stauffacher, C. Rayon, L. Makowski, H.R. Kim, P. Ciesielski, J. Badger, L.N. Paul, D. Kihara, M. Crowley, & M. E. Himmel
- "Towards Plant-specific protein gene function prediction", Akshay Kumar, Ishita Khan, D. Kihara
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183
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"Genome-scale Identification and Characterization of Moonlighting Proteins" (selected oral presentation), Automatic Function Prediction Meeting (AFP-SIG alongside of ISMB 2014), Boston, July 11-12 , 2014
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link
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182
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3D-SIG (alongside of ISMB), Boston, July 11-12 , 2014
- "Predicting protein complex assembly pathway using multiple-protein docking algorithm" (selected oral presentation), Yoichiro Togawa, Juan Esquivel-Rodriguez, Amit Roy, & D. Kihara
- "Fast large scale comparison and structrue fitting for low-resolution electron microscopy maps (poster), Juan Esquivel-Rodriguez & D. Kihara
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link
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181
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PhD thesis defense, Juan Esquivel-Rodriguez, Computer Science, Purdue University, June 18 , 2014
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180
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"Navigating 3D Electron Microscopy Density Maps and Protein Shapes with EM-SURFER and 3D-SURFER 2.0 ", Juan Esquivel-Rodriguez, Yi Xiong, Juan Esquivel-Rodriguez, Xusi Han,
Shuomeng Guang, and Daisuke Kihara, GLBIO 2014 , May 16-18 , 2014
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link
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179
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"Exploring protein interfaces: Steered molecular dynamics and free energy calculations to rank protein-protein docking poses". L.J. Kingsley, J. Esquivel-Rodriguez, D. Kihara, M. Lill, Great Lakes Drug Metabolism & Disposition Group 2014 Meeting, Sheraton Indianapolis City Centre Hotel, Indianapolis, IN, May 15-16 , 2014
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178
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- Logic patterns for finding functionally related genes in Escherichia coli, Ishita Khan, Tiange Dong, Linzi Chen, Weichuan Luo
- Interactive visualization of Gene Ontology hierarchy, Qing Wei
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177
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Undergraduate Research Poster Symposium, Purdue University, April 8, 2014
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link
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176
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Yoichiro Togawa, MS thesis defense, Dept. of Biological Sciences, 1:30pm, Lilly 117, April 11, 2014
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175
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Lecture series in Bioinformatics and Computational Biology, Iowa State University, April 10, 2014
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174
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"Faster Comparison of Electron Microscopy Density Maps of Proteins", Charles Christoffer, Juan Esquivel-Rodriguez, and Daisuke Kihara, Discovery Park Undergraduate Student Poster Session, Hall of Discovery and Learning Research, April 3, 4:30-6:30pm, 2014
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173
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The Office of Interdisciplinary Graduate Programs, Spring Reception Poster Presentation , Purdue University, April 2, 2014
- Assessing Protein Side-Chain Conformation Prediction Methods in Different Residue Environments, Lenna Peterson
- Genome-scale Identification and Characterization of Moonlighting Proteins, Ishita Khan
- Enhanced Electron Microscopy Fitting Using Markov Random Fields, Juan Esquivel-Rodriguez
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link
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172
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Computational modeling of macromolecular structures, Juan Esquivel-Rodriguez, Interdisciplinary graduate program, LWSN3102, Purdue, March 5, 2014
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171
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2nd Zing Protein and RNA Structure Prediction Conference, Cancun, Mexico, Dec. 1-5, 2013
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link
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170
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Beckman Institute, Univ. Illinois at Urbana-Champaign, Oct 28, 2013
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169
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Daisuke Kihara, Department seminar, Dept. of Bilogical Sciences, Purdue University, Oct 2, 2013
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168
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"Prediction of macromolecular structures of protein interactions", Cold Spring Harbor Asia Conferences on Frontiers in Bioinformatics and Computational Biology , Sep 23-27, 2013
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link
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167
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University College London, UK Sep 13, 2013
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166
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2nd ACSL International Summer School, Imperial College London, Sep 8-14, 2013
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165
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"Unified biomolecular 3D surface matching for proteins, ligands, and interactions", Eli Lilly, seminar at Lilly Grand Rounds, Eli Lilly, Indianapolis, Aug 14, 2013
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164
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"3D-SURFER 2.0:Web platform for real-time comparison, visualization and characterization of protein surfaces" Yi Xiong, J. Esquivel-Rodriguez, L. Sael & D. Kihara, Annual Symposium of the Protein Society , Boston, MA, July 20-23, 2013
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163
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Biochemical characterization of an Arabidopsis pectin methylesterase AtPME3 and a pectin methylesterase inhibitor. (poster) F. Senechal, M. L’Enfant, JM Domon, E. Rosiau, P. Marcello, O. Surcouf, J. Esquivel-Rodriguez, A. Mareck, F. Guerineau, H-R. Kim, E. Bonnin, E. Jamet, J. Mravec, D. Kihara, M-C. Ralet, P. Lerouge, J. Pelloux, C. Rayon, The XI Cell Wall Meeting, Nantes, July 7-12, 2013
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162
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"Machine learning approach for protein structure modeling" Telluride Workshop on "Modeling biomolecular structures, interactions and functions", telluride, CO, July 1-5, 2013
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link
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161
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"On protein docking prediction", Seoul National University, Chemistry department, Seoul, Korea, 3pm, June 27, 2013
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160
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"Information flow in biological systems", The 4th International Conference on Statistical Methods in Biomedical Science and Bioinformatics, Chung-Ang University, Seoul, Korea, June 25, 2013
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159
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"Predicting gene function in biological contexts", Seoul National University, Computer Science and Engineering, Seoul, Korea 11am, June 24, 2013
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158
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"Information flow in biological systems", Tokyo Institute of Technology, Tokyo, Japan, June 21, 2013
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157
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"Predictions of structures of protein interactions". D. Kihara, Toyota Technological Institute at Chicago, Chicago, IL, May 20, 2013
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156
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Protein docking prediction guided by predicted protein-protein interface. D. Kihara, B. Li, J. Esquivel-Rodriguez, & D. La, 5th CAPRI (Critical Assessment of Predicted Interactions), Utrecht, the Netherlands, April 17-19, 2013.
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155
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Macromolecular structure modeling and EM fitting. D. Kihara & J. Esquivel-Rodriguez, 5th CAPRI (Critical Assessment of Predicted Interactions), Utrecht, the Netherlands, April 17-19, 2013.
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154
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Predictions of Protein Function, Structures, Dynamics, and Interactions. Bioinformatics and Machine Learning Roundtable, Qatar Computing Res. Institute, Doha, Qatar, March 19-20, 2013.
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153
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EM-LZerD: EM Map Fitting for Multimeric Protein Complexes Using Rotation Invariant Surface Representation. J Esquivel-Rodriguez & D. Kihara Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Keystone Symposia, Lake Tahoe, March 3-7, 2013.
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152
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Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors. D. Kihara, J. Esquivel-Rodriguez. Biophysical Society 57th Annual Meeting, February 2-6, 2013, Philadelphia, PA.
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151
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Macromolecular Structure Modeling and Electron Microscopy Fitting Using 3D Zernike Descriptors. Highlights Track, ISCB-Asia/SCCG 2012, Shenzhen, China, Dec. 17-19, 2012.
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150
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Next generation molecular surface representation for rapid global/local protein shape comparison, docking, and low-resolution data. D. Kihara, National Centers for Biomedical Computing (NCBC) Showcase, Nov. 8-9, Natcher Conference Center, Bethesda, MD
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149
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Binding ligand prediction by comparing local surface patches of potential pocket regions. Zing conference, Mathematical and Computational Medicine, Xcaret, Cancun, Mexico, Dec. 1-15, 2012.
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148
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Local Similarity Search of Physicochemical Properties in Protein-Ligand Binding Sites, Lee Sael & Daisuke Kihara, Translational Bioinformatics Conference (TBC) 2012, Jeju Island, Korea, Oct 13-16, 2012
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147
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Novel quantitative proteomic methods to discover and localize protein complexes., U.K. Aryal, Y. Xiong, E. Mallery, M.C. Hall, J. Xie, D. Kihara, P.N. Baker, D. B. Szymanski, 2012 Plant Genome Awardee Meeting, National Science Foundation, Arlington, VA, Sep. 6-7, 2012.
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146
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Predictions of structures of protein interactions. International Summer School of Life & Health Science, Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Shonan, Kanagawa, Sept. 3-5, 2012
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145
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Biochemical characterization of an Arabidopsis pectin methylesterase AtPME3 and a pectin methylesterase inhibitor. F. Senechal, J-M Domon, M. L’Enfant, D. Tall-Ndoye, J. Esquievel-Rodriguez, F. Guerineau, HR Kim, E. Jamet, E. Bonnin, D. Kihara, M-C Ralet, J. Pelloux, C. Rayon, Gordon Conference on Plant Cell Wall, Colby College, Waterville, ME, August 5-10, 2012
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144
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Invited talk by D. Kihara at Telluride Meeting on Coarse-grained modeling of structure and dynamics of biomacromolecules, Telluride, Colorado, July 23-27, 2012
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143
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A "catalytic dimer" hypothesis for the synthesis of cellulose and other (1,4)-beta-glycans Nicholas C. Carpita (oral presentation), Anna T. Olek, Catherine J. Rayon, Lee Makowski, Shi-you Ding , Peter Ciesielski, Lake Paul, Subhangi Ghosh, Daisuke Kihara, Michael Crowley, Michael Himmel, Jeffrey Bolin,
The 23rd International Conference on Arabidopsis Research (ICAR), Vienna, Austria, July 3-7, 2012
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142
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Invited talk by D. Kihara at Telluride Meeting on Protein folding and Dynamics: From experiment to theory, Telluride, Colorado, June 17-21, 2012
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link
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141
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"Predicting binding ligand and protein docking using surface shape". D. Kihara, Graduate School of Information Science, Tohoku University, Sendai, Japan. May 30, 2012
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140
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"Preditions of structures of protein interactions". D. Kihara, Bioinformatics Seminar series at Institute of Chemical Research, Kyoto University , Uji, Kyoto, Japan. May 28, 2012
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139
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"Systems Level Gene Function Prediction for Assessing Outcome of SNPs", D. Kihara, Chung-Ang University, Seoul, Korea, May 25, 2012
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138
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Great Lakes Bioinformatics Conference (GLBIO) 2012, May 15-17, 2012, Ann Arbor, MI
- "Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors" by J. Esquivel-Rodriguez & D. Kihara
- "Computational characterization of moonlighting proteins using Gene Ontology annotations" by I. Khan, M. Chitale, & D. Kihara
- Special Session, " Proteins in motion: Computational studies in protein flexibility and dynamics" session co-chaired by D. Kihara & L. Kurgan, "Structural features that predict real-value fluctuations of globular proteins" by M. Jamroz, A. Kolinski & D. Kihara
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137
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Chao Yuan, MS Thesis defense "Investigation of optimal residue contact definitions for template-based protein structure prediction", April 10, 3-5pm, 2012, Lilly 1-224, Purdue University
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136
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"Logic Patterns of Homologous Genes Across Species" by Lillian Liu, Huairuo Ren, Yu Leng, Meghana Chitale, Daisuke Kihara, poster presentation at 2012 Undergraduate Research and Poster Symposium, Purdue Memorial Union, North & South Ball Room, April 10 2012, 2-7pm
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135
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"Domain-based protein function prediction in terms of GO vocabulary" by Su Lin Ooi, Meghana Chitale, Ishita Khan, & D. Kihara, Poster presentation at Discovery Park Undergraduate Research Interns (DURI) poster presentation, DLR 131, Purdue University, April 5, 4:30-6:30pm, 2012.
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134
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Invited seminar, D. Kihara, The Research Institute at Nationwide Children's Hospital, Department of Pediatrics, The Ohio State University College of Medicine, March 22, 2012
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133
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"Computational methods for multiple protein docking for asymmetric complexes" (poster: B85, 1315-Pos, 2/27/2012), Juan Esquivel-Rodriguez, Daisuke Kihara, Biophysical Society 56th Annual Meeting, San Diego, Carifornia, Feb. 25-29, 2012 .
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132
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2 poster presentations at Sigma Xi Graduate Student Research Award Competition , Steward Center, Rooms 214/218, Purdue University, Feb. 15 (Wed), 2012 , 12:30-4pm, 6-9pm.
- "Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors" Juan Esquivel-Rodriguez & D. Kihara
- "In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment", Ishita Khan, Meghana Chitale, & D. Kihara
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131
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Oral presentation, "Functional coherence assessment for protein groups and its application to pathway assignment", D. Kihara, Zing conference, IECA (International E. Coli Alliance) 2011 , Xcaret, Cancun, Mexico, Dec. 5-9, 2011
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130
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Invited speaker, "Unified Molecular Representation for Protein Shape Comparison and Interaction", D. Kihara, Zing conference on Protein and RNA Structure Prediction", Xcaret, Cancun, Mexico, Dec. 3-7, 2011
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129
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Ph.D. thesis defense, David La, "Computational models of mutations for predicting and classifying protein-protein interaction sites", Dept. of Bilogical Sciences, Purdue University, Dec. 1, 2011. Presentation available at Ustream video
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link
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128
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Ph.D. thesis defense, Bin Li, "Geometrical Analysis Of Interaction Sites Of Proteins", Dept. of Computer Science, Purdue University, Nov. 29, 2011.
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127
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"Next generation structural bioinformatics and gene function prediction", D. Kihara, Biological Scieces Researh Retreat, Swan Lake resort, Plymonth IN, November 5, 2011
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126
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"Next generation protein 3D structure analysis: Rapid global/local surface comparison, docking, and low-resolution data", D. Kihara, Dept. of Biological Sciences Faculty Research Presentations, Lilly 1-117, Purdue University, 12-1pm, October 27, 2011
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125
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"Protein 3D global/local shape search for function prediction and drug design" by D. Kihara at CS591 (graduate seminar), LWSN B155, Purdue University, October 5, 2011
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124
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Invited Seminar, "Protein surface representation for ligand binding site screening" D. Kihara, Eli Lilly, Indianapolis,October 3, 2011
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123
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Invited Seminar, "Next Generation Protein 3D Structure Analysis: Rapid Global/Local Surface Comparison, Docking and Low-Resolution Data" D. Kihara, University of Alberta, Edmonton, Canada, September 16, 2011
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122
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Invited Seminar,"Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions" D. Kihara, Computational Biology Res. Center, Tokyo, Japan, September 2, 2011
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121
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Purdue University Nano-Bio Student Symposium, MRGN 129, Purdue University, Sept. 1, 2011
- "Protein Docking Prediction Using Predicted Protein-Protein Interface" Bin Li
- "Multi-LZerD: Multiple Protein Docking for Asymmetric Complexes"Juan Esquivel-Rodriguez
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120
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Invited Seminar, "Next generation protein 3D structure analysis: Rapid global/local surface comparison, docking, and low-resolution data", D. Kihara, Fukushima Medical University, September 1, 2011
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119
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Invited Seminar,"Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions" D. Kihara, RIKEN, Yokahama, Japan, August 30, 2011
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118
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ICR Bioinformatics Center, 10 Year Anniversary and New Reconstructing Symposium "Unified molecular representation for protein shape comparison and interaction" D.Kihara, Kyoto University, Uji, Kyoto, Japan, August 29 2011
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117
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Invited Seminar, "Next generation protein 3D structure analysis: Rapid global/local surface comparison, docking and low-resolution data", D. Kihara, Dept. of Computer Science and Engineering, Seoul National University, Seoul, Korea, Building 301, Room 315, August 22, 2011
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116
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ISMB, Viena, Austria, July 15-19, 2011
- AFP-SIG: "Function Prediction for Systems Level: Functional Coherence of Protein Groups and Identification of Missing Genes" M. Chitale, D. Kihara(oral presentation)
- AFP-SIG: "Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches" L. Sael, D. Kihara (poster)
- 3D-SIG: "Multi-LZerD: Multiple protein docking for asymmetric complexes" J. Esquivel-Rodriguez, YD. Yang, D. Kihara(poster)
- 3D-SIG: "Rapid comparison and multimeric protein complex fitting for low-resolution electron microscopy data" D. Kihara, L. Sael, J. Esquivel-Rodriguez (poster)
- 3D-SIG: "Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches" L. Sael, D. Kihara (poster)
- main conference: "Functional coherence assessment for protein groups and its application to pathway assignment" M. Chitale, S. Palakodety, D. Kihara
- main-conference: "Multi-LZerD: Multiple protein docking for asymmetric complexes" J. Esquivel-Rodriguez, YD. Yang, D. Kihara(poster)
- main conference: "Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches" L. Sael, D. Kihara (poster)
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115
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"Protein-protein docking prediction: from pairwise docking, docking interface prediction, and multiple protein docking" by Kihara at workshop on "Modeling Biomolecular Structures, Interactions, and Functions" (organized by Jianpeng Ma, Jeff Skolnick), Telluride, Colorado, June 13-17, 2011.
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114
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4 lectures at International PhD Studies program, Faculty of Chemistry, Warsaw University , Poland, May 23-27, 2011
- May 23 (Mon) "Template-based structure prediction and quality assessment using suboptimal alignments"
- May 25 (Wed) "Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups"
- May 26 (Thr) "Protein-protein docking prediction: from pairwise docking, docking using docking interface information, and multiple protein docking"
- May 27 (Fri) "Binding ligand prediction by Comparing Local Surface Patches of Potential Pocket Regions"
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113
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"Surface Representation for Molecular Global and Local Shape Comparison and Docking", International Institute of Molecular and Cell Biology, Warsaw, Poland, 12:00-13:00, May 25, 2011
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112
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2 poster presentations at International Conference on Structural Genomics , May 10-14, 2011, Toronto, Canada
- "Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions", L. Sael & D. Kihara (received nternational Structural Genomics Organization Poster Prize)
- "Rapid comparison and multimeric protein complex fitting for low-resolution electron microscopy data", J. Esquivel-Rodriguez, L. Sael & D. Kihara
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111
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6 oral presentations at Great Lakes Bioinformatics Conference 2011, May 2-4, 2011, Ohio University, Athens, Ohio
- "Protein-protein Interaction Sites Prediction using Phylogenetic Substitution Models", D. La, D.Kihara
- "Protein Docking Prediction Using Predicted Protein-Protein Interface" Bin Li, D. Kihara
- "Multi-LZerD: Multiple Protein Docking for Asymmetric Complexes" Juan Esquivel-Rodriguez, D. Kihara
- "Rapid Comparison and Multimeric Protein Complex Fitting for Low-Resolution Electron Microscopy Data", Juan Esquivel-Rodriguez, Lee Sael, D. Kihara
- "Patch-Surfer: Alignment Free Surface Patch-Based Ligand Binding Pocket Comparison", Lee Sael, D. Kihara
- "Functional Coherence Assessment for Protein Groups and its Application to Pathway Assignment", Meghana Chitale, D. Kihara
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link
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110
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3 poster presentations at 2011 Undergraduate Research and Poster Symposium , 2:00-7:00pm, April 12 (Tue) 2011, North Ball Room, Purdue Memorial Union, Purdue University
- Fast identification of interacting proteins by considering shape and sequence features(Roshna Agarwal, Lee Sael, D. Kihara)
- SiteHunter: Interactive web application for determining protein ligand binding site location (Yinlong Jin, R. Ren, K. Modi, S. Jain, D. La, D. Kihara)
- Mining association between gene ontology terms by using protein-protein interaction networks(Satwica Yersini, Meghana Chitale, D. Kihara)
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109
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"General framework for multiple protein docking" Juan Esquivel-Rodriguez, D. Kihara, 2011 Interdisciplinary Graduate Program Spring Reception, PMU, Purdue University, April 20, 2011
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108
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3 poster presentations at Discovery Park Student Poster Session, April 6 (Wed) 2011, Hall for Discovery and Learning Research (DLR), 4:30-6:30pm
- Information theoretical approaches for protein sequences and structure, (Yingfei Ma, D. Kihara)
- SiteHunter: Interactive web application for determining protein ligand binding site location (Yinlong Jin, R. Ren, K. Modi, S. Jain, D. La, D. Kihara)
- Docking low-resolution cryo-EM density maps aided by structural homology searching (Wansuk Lim, L. Sael, D. Kihara)
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107
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2 posters at 55st Annual meeting of Biophysical Society, Baltimore MD, March 5-9, 2011 :
- "Novel methods for rapid comparison and multimeric protein complex fitting for low-resolution electron microscopy data", L. Sael, J. Esquivel-Rodriguez, D. Kihara, (March 7, Program #: 1750-Pos, Board #: B660)
- "Local protein surface patch method for protein-ligand binding prediction", L. Sael, D. Kihara (March 8, Program #: 2131-Pos, Board #: B117)
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106
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"Predicting protein function by surface comparison" by Sael Lee, at Bioinformatics seminar, Statistics on Feb 15, 4:30pm, HORT 117, Purdue.
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link
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105
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"Prediction of protein-protein interaction sites, pair-wise, and multiple protein docking", December 20, 2010 , Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing, China
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104
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1 oral presentation and 4 posters at The 21st International Conference on Genome Informatics, Hangzhou, China, December 16-18, 2010 :
- (oral) "Improved Protein Surface Comparison and Application to Low-Resolution Protein Structure Data" L. Sael, D. Kihara
- (poster)"Multiple Protein Docking for Asymmetric Hetero Oligomeric Complexes" J. Esquivel-Rodriquez, Y. Yang, D. Kihara
- (poster) "Functional coherence for protein groups by considering associations between gene ontology terms" Meghana Chitale, Shriphani Palakodety, D. Kihara
- (poster) "Protein Docking Prediction Using Predicted Protein-Protein Interface", Bin Li, D. Kihara
- (poster) "Performance of SUPRB Threading Method in CASP9", Chao Yuan, Mateusz Kurcinski, D. Kihara
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103
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"Binding ligand prediction using local surface Zernike descriptors". December 15, 2010, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
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102
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"Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups". December 15, 2010, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
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101
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"Protein-protein docking prediction: from pairwise docking, docking using docking interface information, and multiple docking". December 14, 2010, Shanghai Jiaotong University, Shanghai, China
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100
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"Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups". December 13, 2010, Fudan University, Shanghai, China
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99
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"Detecting surface shape complementarity for quick identification of interacting proteins", Roshna Agarwal, Paul Justin Tack, Sael Lee, D. Kihara, Grace Hopper Celebration of Women in Computing, Atlanta, Georgia, Sep 28 - Oct 2, 2010
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98
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"A novel method for protein-protein interaction site prediction with phylogenetic substitution models", David La, D. Kihara, The 24th Annual Symposium of the Protein Society, August 1-5, 2010, San Diego, CA, USA.
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97
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Ph.D. thesis defense, Sael Lee, "High throughput screening of global and local protein surfaces.", Dept. of Computer Science, Purdue University, July 16, 2010.
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96
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"Multiple protein docking prediction based on genetic algorithms and physics based scoring", Juan Esquivel-Rodriguez, D. Kihara, 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11-13, 2010, Boston, MA.
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95
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3 presentations at 3DSIG 2010 at ISMB 2010, Boston, July 9-10, 2010:
- (oral) "Real-Time Ligand Binding Pocket Database
- (oral or poster)"Multiple Protein Docking Prediction Method
- (poster) "Fitting Multimeric Complexes into Cryo-EM
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94
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Invited talk "Protein surface representation for structure-based function prediction and docking" by D. Kihara at Telluride workshop on "Coarse-grained modeling of structure and dynamics of biomacromolecules", July 5-9, 2010, Telluride, CO, USA
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93
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Invited talk, "Molecular surface representation for protein shape comparison and docking", D. Kihara, Korea Institute for Advanced Study (KIAS), June 30, 2010, Seoul, Korea.
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92
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Invited talk "Structure of gene functional space in genomes" by D. Kihara at The First International Conference for Industrial Statistics and Bioinformatics, The Research Center for Data Science, Chung-Ang University, Seoul, Korea, June 29, 2010
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91
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"Scoring Functions for Predicting Protein Structure
and Protein-protein Interatcion", Yifeng Yang, Ph.D. thesis defense. Monday, April 19, 2010, 2:00 p.m, LILY 1-117, Purdue University.
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90
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2010 Undergraduate Reserach Poster Symposium, April 7 (Wed), Purdue Memorial Union, 2-6:30pm, Purdue University
- "Why is there a limited number of protein fold in nature?", Abram Magner, Yifeng D. Yang, D. Kihara
- "Classification of local surface shape of ligand binding pockets", Gabriele Martinez, Sael Lee, D. Kihara
- "Structure-basis for protein-DNA interaction", William Hoffmann, D. Kihara
- "Detecting surface shape complementarity for quick identification of interacting proteins", Paul Justin Tack, Roshna Agarwal, Sael Lee, D. Kihara
- "Conservation of sequence and atoimc interactions in ligand binding sites of proteins", Sang Wook Lee, Sael Lee, D. Kihara
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89
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"Comparative study of protein structure prediction methods" Priyanka Surana, D. Kihara, Sigma, 18th Undergradaute Research Day, Apr 3 (Sat), 10am, Lilly Hall,Dept. of Biological Sciences, Purdue University
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88
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"Exploring applications of suboptimal alignments in threading protein structure prediction" Hao Chen, Ph.D. Thesis defense. Apr. 6, 2pm, Lilly 1-117, Purdue University.
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87
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Purdue University Interdisciplinary Graduate Program Reception
- "Unified Protein Docking Procedure with a Shape Complementarity Screening Using 3D Zernike Descriptors and Ranking by Physics-Based Scoring", Juan Esquivel-Rodriguez, et al.
- "Quantification of protein group coherence and pathway assignment in yeast using functional association", M. Chitale et al.
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86
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"Comparative study of protein structure prediction methods" Priyanka Surana, D. Kihara, Sigma, 18th Undergradaute Research Day, Apr 3 (Sat), 10am, Lilly Hall,Dept. of Biological Sciences, Purdue University
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85
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"Comparative study of protein structure prediction methods", Oral presentation of honors students, Priyanka Surana, D. Kihara, March 30, Lilly 1-117, Dept. of Biological Sci., Purdue University
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84
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Sigma Xi Graduate student research presentation, Feb 17 (Wed), 12:30-9pm, Stewart Center, Rm 214/218, Purdue University
- "A statistical method dor comparing flexible protein tertiary structures", Farrukh Arslan, Yifeng Yang, D. Kihara.
- Application of 3D Zernike descriptors to shape-based ligand similarity searching", Padmasini Chakravarthy, V. Venkatraman, D. Kihara
- Quantification of protein group coherence and pathway assignment in yeast using functional association", Meghana Chitale, Shriphani Palakodety, D. Kihara
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83
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"A unified protein docking procedure with a shape complementarity screening using 3D Zernike descriptors", D. Kihara, V. Venkatraman, YD Yang, L. Sael, Biophysical Society meeting, San Francisco, CA, Feb 20-24, 2010
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82
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"Protein surface representation for fast structure search, docking and function prediction", Tokyo Institute of Technology, Dept. of Computer Science, Tokyo, Japan, Dec 28, 2009
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81
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"Protein surface representation for fast structure search, docking and function prediction", Nara Institute of Science and Technology (NAIST), Graduate School of Biological Sciences, Nara, Japan, January 7, 2009
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80
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"A unified protein docking procedure with a shape complementarity screening using 3D Zernike descriptors and ranking by physics-based scoring" CAPRI Critical Assessment of Predicted Interactions 4th Evaluation Meeting, Barcelona, Spain, Dec 9-11, 2009
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79
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"Protein Structure Bioinformatics for Predicting Structure, Docking, and Function" Univ. Cincinnati, Nov. 5, 2009
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78
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"Protein Representation for Efficient Comparison of Surface Properties" (poster) by Sael Lee, 4th Annual KIST/PU Global Research Laboratory Symposium, Sep. 22 (Tue), 8:30-9:30am, Room 214, Steward Center, Purdue University
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77
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PULSe program retreat poster presentation, August 22 (Sat), Beck Agriclutural Center, West Lafayette, IN
- Local surface shape-based protein function prediction using Zernike descriptors, by D. Kihara, Sael Lee & Rayan Chikhi
- Protein structure prediction without optimizing weighting factors for scoring function, by Yifeng D. Yang, Changsoon Park, & D. Kihara
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76
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D. Kihara, "Global and local protein surface comparison and its applications", at TSRC workshop on "Method development for protein structure prediction and design", Telluride Science Res. Center, Telluride, Colorado, June 15-19, 2009.
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75
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Poster presentations at American Society for Microbiology May 17-21, 2009, Philadelphia, PA
- www.EcoliHub.org: An information resource for experimentation and modeling of E. coli K-12, by BL Wanner, WG Aref, T. Conway, KA Datsenko, SC Ess, MR Gribskov, JC Hu, D Kihara, H Mori, D Siegele, DR Whitaker
- N terminal Gly224-Gly411 domain in Listeria adhesion protein (LAP) interacts with receptor Hsp60, by B. Jagadessan, D La, D Kihara, AK. Bhunia
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74
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D. Kihara, Seminars at Statistics Dept, Chung-Ang University, Seoul, Korea, May 14-15, 2009
- May 14: lectures on "Algorithms for biological sequence analysis"
- May 15: research presentation on "Protein surface comparison for function prediction and docking"
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73
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D. Kihara, "Novel bioinformatics approaches for studying protein sequence, structure, and function in omics era", Division of Bio-Medical Informatics, Center for Genome Science, National Institute of Health, Seoul, Korea, May 13, 2009
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72
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The 21st Undergraduate Research Conference at Butler University, Butler University, Indianapolis, IN, April 17, 2009
- Gregg Thomas, "Computational protein function prediction"
- Matt Herron, "Protein Tertiary Structure Universe Viewed from the Perspective of Surface Shape"
- Priyanka Surana, "Comparative study of tertiary structure prediction methods"
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71
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Priyanka Surana, oral presentation on "Computational characterization of proteins having specific cellular localization patterns", Honor thesis oral presentation, Dept. Biological Sciences, Purdue, March 31, 2009.
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70
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SIAM@Purdue Student Conference 09, Stewart Center, Purdue, March 30, 2009
- (oral presentation), Meghana Chitale, 5:30-6pm, Room 313; "ESG: Extended similarity method for automated protein function prediction"
- (oral presentation), Sael Lee, 6-6:30pm, Room 214C; "Protein representation for efficient comparison of surface properties"
- (poster) Bin Li, "Predicting organism of a genome based on word frequences for metagenomics research"
- (poster) David La, "Predicting Protein-Protein Interaction Sites by Computational Modeling of Mutational Patterns"
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69
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Ph.D. thesis defense, Troy Hawkins, Dept. of Biological Sciences, Purdue University, October 6, 2008
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68
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Poster presentations at Biophysical Society 53nd Annual Meeting February 28-March4, 2008, Boston MA
- (3358-Pos/B405, March 4)Local surface shape-based protein function prediction using Zernike descriptors, by D. Kihara, Sael Lee & Rayan Chikhi
- (3371-Pos/B418, March 4)Protein structure prediction without optimizing weighting factors for scoring function, by Yifeng D. Yang, Changsoon Park, & D. Kihara
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67
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Seminar at the Biochemistry seminar series "Annotating protein structures by surface shape comparison" by D. Kihara, Feb 27th, 11:30-12:15, WTHR 201
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66
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Sigma-Xi graduate students poster presentation, Feb. 18 (Wed) afternooon, Steward Center, Rooms 214/218, Purdue Univ.
- ESG: Extended similarity group method for automated protein function prediction, by M. Chitale et al.
- Protein representation for efficient comparison of surface properties, by Sael Lee et al.
- Improvement of template-based protein structure prediction by suboptimal alignments, by Hao Chen et al.
- Threading without optimizing weighting factors for scoring function, by Yifeng D Yang et al.
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65
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Guest lecture on our research projects in protein bioinformatics at CS 197 Honors Seminar, Feb 16, 9:30-10:20, LWSN B134.
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64
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Workshop organizer and oral presentation at e-Bioinformatics Workshop at IEEE e-Science '08, Dec. 12, IUPUI University Conference Center & Hotel, Room 232 "Annotating Protein Structures by Surface Shape Comparison" by D. Kihara
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63
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Daisuke Kihara, Depatmental Seminar at Biological Sciences, Purdue Univesity, "Informatics approaches for studying protein sequence, structure, and function in omics era, Oct. 15, 2008
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62
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Matt Herron, Brian Denton, David La, D. Kihara, "The protein structure universe viewed from the perspective of surface shape", The 19th Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics, Argonne National Laboratory, November 7, 2008
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61
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"Protein representation for efficient comparison of surface properties" Sael Lee, Bin Li, David La, Raif Rustamov, Daisuke Kihara, (poster presentation), 2008 Grace Hopper Celebration of Women in Computing, Keystone, Colorado, Oct 1, 2008.
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60
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Presentations for Graduate student orientations 2008:
- Biology: Poster presentation by Troy Hawkins, main lobby in Lilly Hall, August 19, 3:30-5:00PM.
- CS: Two poster presentations by Sael Lee and Meghana Chitale, at Research Showcase, 11am-12:30pm, September 8 (Mon), 2008, Buchanan room, Ross Ade Stadium, 5th floor, Purdue.
- PULSe: Two poster presentations by Hao Chen and Yifeng Yang, at PULSe retreat, John S. Wright Forestry Center at Martell Forest, West Lafaytte, August 23, 2008,
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59
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ISMB 2008, Toronto, Canada, July 19-23, 2008. Two posters:
- Automated protein function prediction using Extended Similarity Group (ESG) of sequences. M. Chitale, T. Hawkins, C. Park, D. Kihara.
- EcoliHub: An information resource for experimentalists and modelers. DR Whitaker, WG Aref, KA Datsenko, S Ess, MR Gribskov, D Kihara, S Kim, H Mori, A Roumani, BL Wanner.
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58
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Oral presentation at AFP/Biosapiens 2008(Automated Function Prediction special Interesting Group at ISMB2008), July 18-19, Toronto, Canada, "ESG: Extended Similarity Group Method for Improved Automated protein Function Prediction" by Meghana Chitale, Troy Hawkins, Changsoon Park & D. Kihara.
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57
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Preston Spratt, Honors research presentation, "Structure modeling of E. coli proteome", March 27, 20008, Lilly 3-418, 5:30pm, Dept. of Biological Sci, Purdue University.
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56
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2008 Undergraduate Research and Poster Symposium, 2-7pm, March 31, 2008, Purdue Memorial Union Ballrooms.
- Priyanka Surana, Yifeng Yang, D. Kihara "Computatinal modeling of ABC transporters"
- Rupal Trivedi, Yifeng Yang, D. Kihara, "Disorder region prediction of E. coli proteins"
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55
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Invited talk "Quality assessment of template-based protein structure prediction", Dept. of Bioengineering, University of Illinois at Chicago, College of Medicine West, Room 221, 1853 W Polk St., Chicago, IL, February 26, 2008
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54
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Poster presentations at Biophysical Society 52nd Annual Meeting February 2-6, 2008, Long Beach, CA
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53
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(3250-Pos/B553)Predicting the error of template-based protein structure modeling by suboptimal alignment stability, by Hao Chen & D. Kihara
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52
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(3282-Pos/B585)A fast methodology for high throughput comparison of tertiary structure and physicochemical properties, by D. Kihara, Sael Lee, Bin Li, David La, Raif Rustamov
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51
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Invited talk "Template-based protein structure prediction and beyond" at Korea Institute of Science and Technology Information (KISTI), December 26, 2007, Daejeon, Korea
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50
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Invited talk "Computational protein structure and function prediction" at Chung-Ang University, December 27, 2007, Seoul, Korea
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49
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7th KIAS-Soongsil Conference, October 4-6, 2007, Soongsil Univ., Seoul, Korea, "Protein function prediction for proteomics era (invited talk) "
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48
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Structural Biology Seminar Series, Dept. of Biolgical Sciences, Purdue University, September 19, 2007, 1:30-2:20pm, Lilly Hall, 1-117, Dept. of Biological Sciences, Purdue University, " Predicting protein function from sequence: theory and applications ", by Troy Hawkins
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47
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Structural Biology Seminar Series, Dept. of Biolgical Sciences, Purdue University, September 26, 2007, 1:30-2:20pm, Lilly Hall, 1-117, Dept. of Biological Sciences, Purdue University, "Error estimation for template-based protein structure prediction ", by Hao Chen
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46
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Biomedical Engineering Society Annual Meeting, September 26-29, 2007, Los Angeles, CA, "A fast method for high throughput comparison of tertiary structure and physicochemical properties (talk) " in the Bioinformatics and Systems Biology track (Session co-chair: Kihara)
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45
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The 21st Symposium of the Protein Society, July 21-25, 2007 Boston, MA
- (poster #268)"Protein surface representation for fast comparison of tertiary structure and physicochemical properties" by S. Lee, B. Li, D. La, R. Rustamov & D. Kihara (July 23)
- (poster #464)"High-throughput function assignment for proteomics datasets with PFP" by T. Hawkins, M. Chitale & D. Kihara (July 24)
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44
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ISMB 2007, July 21-25, 2007 Vienna, Austria
- (talk)"Enriching functional knowledge in proteomics data using high-throughput PFP prediction", by T. Hawkins, M. Chitale & D. Kihara, AFP/Biosapiens Special Interest Group, July 20, 2007
- (poster)"Functional enrichment of proteomics datasets with PFP", T. Hawkins, M. Chitale, S. Luban & D. Kihara.
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43
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Indy '07: Indy Regional Bioinformatics Conference, May 31-June 2, 2007,
- (selected talk) H. Chen & D. Kihara, "Estimating quality of template-based protein models by alignment stability"
- (poster) T. Hawkins, M. Chitale, S. Luban, & D. Kihara, "Function prediction for proteomics datasets using PFP"
- (poster) M. Chitale, T. Hawkins & D. Kihara, "Development of methods for missing enzyme/gene prediction with PFP"
- (poster) S. Lee, D. La, B. Li, R. Rustamov, D. Kihara, "A fast methodology for high throughput comparison of tertiary structure and physicochemical properties"
- (poster) B. Li, S. Turuvekere, M. Agrawal, K. Ramani & D. Kihara, "Local geometry characterization of protein surfaces with the visibility criteria"
- (poster) P. Spratt, S. Krawczyk, Y.D. Yang & D. Kihara, "EcoliPredict: structure modeling of E. coli proteome"
- (poster)Y.D. Yang & D. Kihara, "Threading without training weighting factors for scoring functions"
- (poster)L. Si, D. Yu, D. Kihara & Y. Fang, "Using sequence similarity scores for automatic gene function annotation in the biomedical literature"
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42
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Program Committee member and Session Chair at Interface 2007: the 39th Symposium on the interface of statistics, computing science, and applications, May 23-26, 2007, Doubletree Hotel, Philadelphia,"Computational techniques for structural genomics (session title)", "Surface shape-based protein structure classification and search (talk) ", Daisuke Kihara
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41
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" Protein function and structure prediction for proteomics analyses " Invisted talk at Indiana University, Informatics Department, May 3, 2007, Bloomington, IN
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40
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The Computer Research Insistute Poster Presentation, April 5, 2007, 4-6pm, Atrium of MSEE building, Purdue Univeresity, "Structure modeling of E. coli proteome: Quality Evaluation ", Preston Spratt, Steve Krawczyk, Yifeng Yang & Daisuke Kihara
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39
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2007 Undergraduate Research and Poster Symposium, April 4, 2007, College of Science, Agriculture, Engineering, and Technology, Purdue University,
- "Structure modeling of E. coli proteome: Homology models" by Steve Krawczyk, Preston Spratt, Yifeng Yang & D. Kihara
- "Structure modeling of E. coli proteome: Quality Evaluation" by Preston Spratt, Steve Krawczyk, Yifeng Yang & D. Kihara
- "Benchmark of new amino acid similarity matrices on recognition of distant protein structures" by Yu-Hsuan Rex Cheng, Hao Chen & D. Kihara
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38
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Dept. of Biological Science Undergraduate Research Presentation, March 31, 2007, Lilly Hall, Purdue University,"Structure modeling of E. coli proteome: Quality Evaluation ", Preston Spratt, Steve Krawczyk, Yifeng Yang & Daisuke Kihara
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37
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Nara Institute of Science and Technology, Nara, Japan, December 28, 2006,"Advanced techniques for protein function prediction and protein tertiary structure search for proteomics analyses", Daisuke Kihara
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36
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One-day course on bioinformatics , Graduate program, Kansai Medical University, Osaka, Japan, December 25, 2006, "Bioinformatics: Introduction and advanced topics", Daisuke Kihara
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35
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Ajinomoto Life Science Institute, Kawasaki, Japan, December 22, 2006, "Advanced techniques for protein function prediction and protein tertiary structure search for proteomics analyses", Daisuke Kihara
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34
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Critical Assessment of Techniques for Protein Structure Prediction (CASP7) November 26-30, 2006, Asilomar Conference Center, CA, Invited talk in Function prediction category,Daisuke Kihara
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33
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BMES2006: (Biomedical Engineering Society Annual Meeting 2006) "Systems Biology and Bioinformatics" Track Oct. 12-14, 2006, Hyatt Regency Chicago, Chicago, IL "Computational techniques for genomics, proteomic, structural and pathway data" session, Oct. 12, session co-chair with Dr. Christina Chan, "Enhanced protein function prediction for proteomics analysis", Daisuke Kihara (invited talk)
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32
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Center for Comp. Biology & Bioinformatics Seminar Series, October. 6, 2006, Medical Science Building Rm326, 3:30-4:30, Indiana Univ. School of Medicine, Indianapolis, IN,"Predicting protein function from sequence and structure", Daisuke Kihara (invited talk)
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31
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The Second Automated Function Prediction Meeting, August 30 - September 1 2006, Cal-(IT)2 buidling, UC San Diego, CA,"PFP: sequence-based annotation of sequences and local sequence motifs with contextual GO term association", Troy Hawkins, Stan Luban & Daisuke Kihara (poster)
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30
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Symposium on "Protein motion for function and folding(temporal title)", September. 28-29, 2006, Institute for Protein Research, Osaka University, Japan, "Low-resolution and uncertainty in protein function and structure prediction", Daisuke Kihara (invited talk)
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29
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TeraGrid '06, June 12-15, 2006, Indianapolis, IN,
- "EMD: an ensemble DNA regulatory motif discovery algortihm for Grid computing.", Yifeng D. Yang, Jianjun Hu & Daisuke Kihara
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28
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The Third Annual Indiana Bioinformatics Conference, May 19-20, 2006,Center for Computational Biology and Bioinformatics, Indiana Univ. School of Medicine,
- "Bridging geometric protein surface features and phylogenetic information for rapid identification of protein-protein interaction interfaces(invited oral presentation)", David La, Dennis Livesay & Daisuke Kihara
- "PFP: sequence-based annotation of sequences and local sequence motifs with contextual GO term asssociation(invited oral presentation)", Troy Hawkins, Stan Luban, & Daisuke Kihara
- "Template-based protein structure prediction with a reliability measure for structural genomics era(poster)", Hao Chen, Yen Hock Tan, & Daisuke Kihara
- "Ligand binding site prediction with the visibility criteria(poster)", Bin Li, S. Thruvekere, M. Agrawal, K. Ramani & Daisuke Kihara
- "Multi-resolution protein representation for fact protein structure searching(poster)", Sael Lee, Bin Li, David La, Raiv Rustamov, & Daisuke Kihara
- "On the effect of long-range interactions on the secondary structure formation of proteins(poster)", Daisuke Kihara
- "Coiled-coil structures in E. coli interactome (poster)", Stan Luban, Akiyasu Yoshizawa & Daisuke Kihara
- "Neural network based protein domain prediction (poster)", Yen Hock Tan, Otoniel Venezuela, Evans A. Tapia & Daisuke Kihara
- "Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences (poster)", Yen Hock Tan, He Huang & Daisuke Kihara
- "Accounting for natural flexibility in protein structure prediction comparisons(poster)", Jairav Desai & Daisuke Kihara
- "EcoliPredict: bioinformatics prediction resource for EcoliHub (poster)", Barry Wanner, Daisuke Kihara, Troy Hawkins & Yifeng D. Yang
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27
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American Society for Microbiology ASM-FEMS Conference on Protein Traffic in Prokaryotes, , May 6-10, 2006, Crete, Greece,
- "EcoliPredict: Bioinformatics prediction resource for EcoliHub.", Barry Wanner, Daisuke Kihara, Troy Hawkins & Yifeng D. Yang
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26
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Undergraduate Research Poster Presentation, April 11, 2006, College of Science, Purdue Univ.,
- "Use of Neural Network for Protein Domain Prediction", Yen Hock Tan & Daisuke Kihara
- "Including Natural Protein Fexibility in Predicted Protein Structure Comparisons", Jairav Desai & Daisuke Kihara
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25
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2006 Sigma Xi Graduate Studnet ReserachPoster Presentation, Feb. 14, 2006, Stewart Center Rm 214, Purdue, Poster presentations:
- "Protein Structure-Sequence Alignment with a Reliability Measure "(H.Chen, D. Kihara),
- "A New Perspective on an Old Tool: Extending the Coverage of Sequence Similarity-Based Function Prediction with PFP "(T.B.Hawkins, S.Luban, D.Kihara),
- "Bridging Geometric Protein Surface Features and Phylogenetic Information for Rapid Indentification of Protein-Protein Interaction Interfaces "(D.La, D. Liversay, D. Kihara),
- "Multi-Resolution Protein Representation" (S.Lee, B.Li, D. La, R. Rustamov, D.Kihara),
- "Ligand Binding Sites Prediction with the Visibility Criteria "(B.Li, S.Turuvekere, M.Agrawal, K.Ramani, D.Kihara)
- "EMD: An ensemble algorithm for discoverying regulatory motifs in DNA sequences. "(Y.D.Yang, J.Hu, D. Kihara)
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24
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Bioinformatics Seminar Series, , January 24 (Tue), 2006, Mechanical Engineering Building ME161, 4:30-5:30, Purdue University, "Enhanced Automated Function Prediction for Proteomics Analysis", Daisuke Kihara
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23
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The 16th International Conference on Genome Informatics, Dec. 19-21, 2005, Yokohama, Japan, Poster presentations:
- "Dependence of the Accuracy of Protein Secondary Structure Prediction on Long-Range Interactions "(D. Kihara),
- "Protein-Protein Docking Algorithm Using Pre-Identified Binding Site Patches"
- "Ligand Binding Sites Prediction with the Visibility Criteria "(B.Li, S.Turuvekere, M.Agrawal, K.Ramani, D.Kihara),
- "A New Perspective on an Old Tool: Extending the Coverage of Sequence Similarity-Based Function Prediction with PFP "(T.B.Hawkins, S.Luban, D.Kihara),
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22
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International Symposium "From Genomics to Chemical Genomics: 10th Anniversary of KEGG, Dec. 15-16, 2005, PALULU Plaza, Kyoto, Japan, "Protein function prediction in the Structural Genomics Era", Daisuke Kihara (invited talk)
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21
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International Symposium on Frontiers of Computational Science 2005, Dec. 12-13, 2005, Noyori Conference Hall, Nagoya University, Japan, "Protein function prediction in the Proteomics Era",Daisuke Kihara (invited talk)
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20
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Structural Biology Seminar, November 16, 2005, Department of Biological Sciences, Purdue University, "Protein function prediction methods beyond BLAST search", Daisuke Kihara
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19
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Computer Research Institute Seminar, October 19, 2005, Computing Reserach Institute, Purdue University, "Protein function prediction in Structural Genomics Era", Kihara
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18
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16th Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics, November 4-5, 2005, Argonne National Laboratory
- "Evaluation and Development of Protein Function Prediction", Stan Luban
- "Using Neural Network in Protein Domain Prediction", Yen Hock Tan
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17
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Mini-Workshop on Computational Studies on Proteins, September 8, 2005, Children's Hospital Research Foundation, Cincinnati, Ohio, "Protein function prediction from sequence and structure", Daisuke Kihara (invited talk)
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16
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PULSe Retreat, August 20, 2005, John S. Wright Forestry Center at Martell Forest, "Computational Function Prediction", Troy Hawkins, Stan Luban, Daisuke Kihara
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15
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Biology Department New Graduate Students Orientation, August 12, 2005, Lilly Hall of Life Sciences, Purdue University, "Bioinformatics Research in Kihara Lab", Daisuke Kihara
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14
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2005 Summer Undergraduate Research Fellowship (SURF) Poster Presentation, August 2 2005, MSEE Atrium, Purdue University
- "Protein-Protein Interaction Data Assessment", Ei Ei Phyu
- "Comparative Study of Small RNA and Small Peptides in Complete Genome Sequences", Stan Luban
- "BioQ: A 3D Querying Engine for Proteins", Athurva Goa
- "Comparison of Distantly Related Protein Sequence Alignments with Multiple Amino Acid Similarity Matrices", Yen Hock Tan
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13
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Marc/Aim Research Presentation, July 28 2005, Burton Morgan Center for Entrepreneurship, "Protein Structure Prediction with ZDOCK 2.3", Luis Avila, Bin Li, Daisuke Kihara
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12
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ISMB, June 25-29 2005, Detroit, Michigan
- "The use of context-based functional association in automated protein function prediction methods", Troy Hawkins, Daisuke Kihara
- "PFP: Automatic annotation of protein function by relative GO association in multiple functional contexts", Troy Hawkins, Daisuke Kihara
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11
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Midwest Computational Structural Biology Workshop, April 30 – May 1, 2005, Brook Lodge, Michigan State University, Augusta, Michigan
- "Voxelized Protein Model for Fast Protein Docking and Function Prediction", Srinivasan Turuvekerel, Manish Agrawal, Karthik Ramani, Daisuke Kihara
- "Protein Structure-Sequence Alignment with a Reliability Measure", Hao Chen, Daisuke Kihara
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10
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Guest lecture at BIOL 517 (Molecular Biology: Proteins), April 13 2005, Lilly Hall of Life Sciences, Purdue University, "Computational Protein Structure Prediction Methods", Daisuke Kihara
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9
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Undergraduate Research Poster Presentation, College of Science & College of Agriculture, April 11, 2005, PMU Faculty Lounges, Purdue University
- "Comparing Tertiary Structures of Protein Active Sites", Yuhao Lin
- "Comparative Study of Small RNA and Small Peptides in Complete Genome Sequences", Stan Luban
- "Computer Graphics Program in Foreign Language Instruction", Ei Ei Phyu
- "Comparison of Distantly Related Protein Sequence Alignments with Multiple Amino Acid Similarity Matrices", Yen Hock Tan
- "Structure-basis of protein-protein interaction", Brian Trisler
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8
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The thirteenth Annual Undergraduate Research Day, Dept of Biological Sciences, April 2, 2005, Lilly Hall of Life Sciences, Purdue University, "Comparative study of small RNA and small peptides in complete genome sequences", Stan Luban
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7
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Biochemistry Division Seminar, April 1 2005, "Toward a better template-based protein structure prediction", Daisuke Kihara
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6
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Biology Honors Research (BIOL 497) Presentation, March 31 2005 , Lilly Hall of Life Sciences, Purdue University, Stan Luban
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5
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PULSe Graduate Students Recruitment, March 5 2005, Hansen Hall, Purdue University, "Protein Sequence-Structure Alignment with a Reliability Measure", Hao Chen
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4
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CS department Graduate Student Recruitment, March 5 2005, Computer Science Building, Purdue University, "Bioinformatics Research in Kihara group", Daisuke Kihara
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3
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Biology Graduate Students Recruitment, February 26 2005,"Research in Kihara Bioinformatics Lab!", Troy Hawkins
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2
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Sigma Xi Graduate Student Research Poster Presentation, February 17 2005, Steward Center, Purdue University
- "Protein Sequence-Structure Alignment with a Reliability Measure", Hao Chen
- "A structured approach to computational protein function prediction", Troy Hawkins
- "A novel method for constructing phylogenetic trees based on complete genome sequences", Bin Li
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1
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15th Annual Argonne Symposium for Undergraduates in Science,Engineering and Mathematics, November 5-6, 2004, Argonne National Laboratory, "Improvement of Protein Sequence Alignments for Better Protein Structure Prediction", Yen Hock Tan
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