Presentations

Upcoming Presentations

# Presentation Relevant Links
1 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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2 Invited talk: at Gordon Research Conference on Three Dimensional Electron Microscopy, Newry, ME, United States, June 11-16, 2023
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3 The Kuntz Symposium, ACS National Fall meeting, San Francisco, CA, United States, August 13-17, 2023

Past Presentations

# Presentation Relevant Links
325 One World Cryo-EM online seminar, October 5, 2022
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324 Genki Terashi, "Protein Structure Modeling and Quality Evaluation from Cryo-EM maps Using DAQ Score", RIKEN, Japan, October 5, 2022
323 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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322 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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321 Invited talk, Workshop on Machine Learning in cryo-EM, National University of Singapore, September 19-23, 2022
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320 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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319 Genki Terashi, "Residue-wise local quality estimation for protein models from cryo-EM maps", Osaka University, Japan, September 12, 2022
318 Invited talk, Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules, Telluride CO, July 25-29, 2022
317 Eman Alnabati, PhD thesis defense, "Protein Structural Modeling Using Electron Microscopy Maps", Purdue University, July 14, 2022
316 "Protein structure modeling and model quality assessment for cryo-EM density maps using deep learning", Nagoya University, July 6, 2022
315 "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
314 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
313 ODSS Software Tools for Open Science 2022, NIH, virtual meeting, June 2-3, 2022
312 Sai Raghavendra Maddhuri Venkata Subramaniya, PhD thesis defense,"Deep learning enabled 3D protein structure modeling", Purdue University, May 16, 2022
311 Presentations at the Hitchhiker's Guide to the Biomolecular Glaxy 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
310 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
309 Lyman Monroe, PhD thesis defense, "Molecular dynamics in protein structure quality assessment and refinement", Purdue University, April 6, 2022
308 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
the 4th International Symposium on Cryo-3D Image Analysis 2022
307 "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
306 Invited talk "Protein 3D structure modeling from medium-resolution cryo-EM density maps" at Pacifichem 2021 , Honolulu, Hawaii December 16-17, 2021
Pacifichem 2021
305 "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
304 Talk by Genki Terashi, The 49th QSAR Symposium, The Pharmaceutical Society of Japan (virtual conference), Nov 18-19, 2021
303 "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
302 "Computational protein docking modeling with application of deep learning", Vellore Institute of Technology (VIT), India, Nov. 17, 2021
301 "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
300 "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
299 "Deep learning-assisted protein 3D structure modeling for medium resolution cryo-EM density maps", Rossmann Symposium, Purdue University, Oct. 25, 2021
298 "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
297 "Deep learning-assisted protein 3D structure modeling for medium resolution cryo-EM density maps", Invited talk at University of Washington, Seattle,Oct. 12 , 2021
296 "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
295 Invited talk "Protein structural bioinformatics after CASP14" at Informatics in Biology, Medicine and Pharmacology (IIBMP) Tokyo, Japan, Sep. 27-29, 2021
294 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
293 Keynote talk "Deep-learning-assisted protein 3D struture modeling for medium-resolution cryo-EM density maps", D. Kihara, BIOKDD 2021 , Aug 15, 2021
Biokdd 21
292 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
291 "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
290 "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
289 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.
The Hitchhiker's Guide to the Biomolecular Galaxy 2021
288 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
2021 65th Biophysical Society Annual Meeting
287 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
286 "Protein 3D structure modeling for medium-resolution cryo-EM density maps", Online Seminar at the CMU-Pitt CPCB Seminar series, October 30, 2020
CMU-Pitt CPCB Seminar series
285 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
5th Annual Southern California Cryo-EM Symposium
284 Deep learning for detecting 3D structures of biomolecules, Data Science and Machine Learning seminar series, Purdue Fort Wayne, October 6th, 2020
283 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
ISMB 2020
282 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
281 Purdue CS department, PhD Visit Day, area talk and a poster, March 2, 2020
280 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
279 "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
278 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
277 "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
276 "Computational protein tertiary structure modeling from cryo-EM maps of intermediate resolution", D. Kihara, Dept. of Physics, Purdue University, Sep 10, 1:30pm, PHS242
275 invited talk (Kihara), Latin American High Performance Computing Conference (CARLA) 2019, University of Costa Rica, Sept 25-27, 2019
274 "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
273 "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
272 "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
M&M 2019 Microscopy & Microanalysis
271 "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
XV Cell Wall Meeting
270 "Computational protein tertiary structure modeling from cryo-EM maps, protein docking, and protein 3D shape analysis", AIST, Tokyo, Japan, July 11, 2019
269 "Computational protein tertiary structure modeling from cryo-EM maps of intermediate resolution", RIKEN, Waco, Japan, July 8, 2019
268 "Computational protein tertiary structure modeling from cryo-EM maps of intermediate resolution", Tohoku University, Dept. of Computer Science, Sendai, Japan, July 5, 2019
267 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
266 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
2019 Purdue Hitchhiker's Guide to the Biomolecular Galaxy Symposium
265 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
Missouri Symposium in Molecular Biophysics, Structural Electron Microscopy
264 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
263 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
16th Annual Conference of the Midsouth Computational Biology & Bioinformatics Society (MCBIOS '19)
262 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
2019 Annual Biophysical Society Meeting
261 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
Sigma Xi Purdue Chapter poster competition
260 Computational prediction of protein toxicity from sequence using gene ontology terms(oral), Aashish Jain & D. Kihara, 2019 ASM Biothreats, Jan 29-31, 2019
2019 ASM Biothreats
259 CASP13 evaluation meeting, Round table discussion on CAPRI protein docking session, Cancun, Mexico, Dec. 1-4, 2018
CASP13 evaluation meeting
258 "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
257 "Computational modeling of protein-protein interactions", Indiana University, Dept. of Chemistry, Bloomington, Oct 16 (Tue), 2018
"Computational modeling of protein-protein interactions"
256 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
Purdue Institute for Drug Discovery, 5th Annual Symposium
255 "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
"Computational protein structure modeling for high to medium resolution cryo-electron microscopy density maps"
254 "Computational prediction and modeling for protein-drug and protein-protein interactions", The University of Alabama at Birmingham, Sept. 14, 2018
253 "De novo protein structure modeling for cryo-EM maps", Coarse-grained modeling of structure and dynamics of biomacromolecules, Telluride, CO, July 23-27, 2018
Coarse-grained modeling of structure and dynamics of biomacromolecules
252 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
3D-SIG at ISMB
251 "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
250 "Computational protein structure modeling for medium to low resolution cryo-EM density maps", D. Kihara, AIST, Tokyo, June 25, 2018
249 "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
Hitchhiker's Guide to to the Biomolecular Galaxy
248 "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
Purdue Undergraduate Research Poster Symposium
247 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
62nd Biophysical Society Annual Meeting
246 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
245 "Computational protein structure modeling for medium to low resolution cyro-electron microscopy density maps", Daisuke Kihara, Biochemistry Seminar, Purdue University, Jan. 16, 2018
244 "Structure modeling of disordered protein interactions", D. Kihara, the 4th International conference on protein & RNA structure prediction, Montego Bay, Jamaica, Dec. 5-8, 2017
243 modeling report at CryoEM Structure Challenges Workshop, Stanford Univ., CA, Oct 6-8, 2017
CryoEM Structure Challenges Workshop
242 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
ISMB 2017
241 "Computational modeling of various types of protein complexes", July 14, 2017, AIST, Tokyo, Japan
240 "In silico screening of biomolecules", July 12, 2017, Ono Pharmaceutical, Kyoto, Japan
239 "Molecular surface-based in silico screening of biomolecules", July 10, 2017, Teijin-Pharma, Tokyo, Japan
238 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
237 Daisuke Kihara, "Computational modeling of flexible protein-protein and protein-drug interactions", Computational Biophysics to Systems Biology (CBSB2017), Cincinnati, Ohio, May 18-20, 2017
Computational Biophysics to Systems Biology (CBSB2017)
236 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"
Great Lakes Bioinformatics Conference (GLBIO) 2017
235 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"
The Hitchhikers' Guide to the Biomolecular Galaxy
234 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"
Tessman Symposium
233 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
232 Lenna X. Peterson, PhD Thesis defense, "Computational modeling of multifarious protein interactions", NLSN 1215, Purdue University, Apr 6, 2017
231 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
230 Woong-Hee Shin, Structural Biology Seminar, Purdue University, Feb. 1 2017
229 "In silico screening and modeling of protein-drug and protein-protein interactions", Albert Einstein College of Medicine, New York, NY, Jan. 24 , 2017
Albert Einstein College of Medicine
228 12th Critical Assessment of Techniques for Protein Structure Prediction (CASP12) Evaluation meeting, CAPRI docking & Quality assessment round table Gaeta, Italy, December 10-13, 2016
CAPRI docking & Quality assessment round table
227 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
226 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
225 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
Bioinformatics seminar, Purdue University
224 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
223 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
222 Ishita Khan, Ph.D. thesis defense, Dept. of Computer Science, LWSN building, Room 1142, Purdue University, 1pm, July 25, 2016
221 "The Boltzmann Sequence-Structure Channel" by A. Magner, D. Kihara, & W. Szpankowski, IEEE International Symposium in Information Theory, Barcelona, Spain, July 10-15, 2016
IEEE International Symposium in Information Theory
220 "Ensemble-based evaluation for protein structure models" (oral presentation), ISMB, Orlando Florida,July 10-12, 2016
ISMB
219 "Considering chain flexibility in protein structure evaluation" (oral presentation), 3D-SIG, Orlando Florida,July 8-9, 2016
3D-SIG
218 "Genome-scale prediction of moonlighting proteins using diverse protein association information" (oral presentation), Function-SIG at ISMB, Orlando Florida,July 9, 2016
Function-SIG at ISMB
217 "PL-PatchSurfer: Molecular surface-based virtual screening program", National Institute of Advanced Industrial and Science, Tokyo Japan, June 17, 2016
216 D. Kihara, Molecular modeling of energy storage devices & Biomolecular complexes, CERM 2016 47th Central Region Meeting of American Chemical Society, May 19, 2016
CERM 2016
215 D. Kihara, "Ensemble-based evaluation for protein structure models" The 3rd International Conference on Mathematical & Computational Medicine May 16-18, 2016
The 3rd International Conference on Mathematical & Computational Medicine
214 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
The Hitchhiker's guide to the biomolecular galaxy
213 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
6th CPARI protein docking prediction evaluation meeting
212 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
211 D. Kihara, "Computational docking of multifarious protein complexes", Dept. of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Feb. 29, 2016
210 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
60th Biophysical Society meeting
209 D. Kihara, 3rd International Conference on Protein and RNA Structure Prediction, Punta Cana, Dominican Republic, Dec. 14-18, 2015
208 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
207 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
"Patch-Surfer and PL-PatchSurfer: Predicting binding ligands for target proteins by molecular surface similarity and complementarity"
206 D. Kihara, The 15th KIAS Conference on Protein Structure and Function, Seoul, Korea Sept. 17-19 , 2015
The 15th KIAS Conference on Protein Structure and Function
205 D. Kihara, "On the origin of protein superfamilies and superfolds", 4th SNU Bioinformatics Workshop, Seoul National University, Seoul, Korea, August 18-19, 2015
4th SNU Bioinformatics Workshop
204 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
3D-SIG 2015
203 D. Kihara,"Gene function prediction in biological contexts", Hokkaido University, Sapporo, Japan, July 2 , 2015
202 "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
The 15th Annual Meeting of the Protein Science Society of Japan
201 "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
200 "Multi-residue scoring function for selecting decoys in protein structure prediction", D. Kihara, The Chem-Bio Informatics Society, Tokyo, Japan, June 22, 2015
The Chem-Bio Informatics Society
199 "Comparison and fitting of molecular shapes for low-resolution structural data" D. Kihara, RIKEN, Yokohama, Japan, June 19, 2015
198 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
Great Lakes Bioinformatics Conference
197 "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
From Computational Biophysics to Systems Biology (CBSB2015)
196 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
A Purdue Mini-symposium on Integrated Structure, Function, and Interactions of the Protein Universe"
195 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
194 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.
the 59 th Biophysical Society Annual Meeting
193 "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.
Information Theory and Applications
192 Local image comparison using Krawtchouk moment invariants. A. Sit & D. Kihara, 2015 Joint Mathematics Meetings, San Antonio, Jan. 12, 2015
Joint Mathematics Meetings, San Antonio
191 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
CASP11
190 "Exploring protein-ligand interactions using molecular local surface comparison methods." Dept. of Chemistry, Purdue University, Dec. 5, 2014
189 Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules, Telluride, CO, Aug 4-8, 2014
Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules
188 "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
187 "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.
186 "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
The Biological and Biomedical Consequences of Protein Moonlighting
185 "Why Protein Folds and Superfamilies have Skewed Distributions?" Zing Conference on Protein Folding, July 16-19, 2014, Punta Cana, Dominican Republic
Zing Conference on Protein Folding
184 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
183 "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
Automatic Function Prediction Meeting
182 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
3D-SIG
181 PhD thesis defense, Juan Esquivel-Rodriguez, Computer Science, Purdue University, June 18 , 2014
180 "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
GLBIO 2014
179 "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
178
  • 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
177 Undergraduate Research Poster Symposium, Purdue University, April 8, 2014
Undergraduate Research Poster Symposium
176 Yoichiro Togawa, MS thesis defense, Dept. of Biological Sciences, 1:30pm, Lilly 117, April 11, 2014
175 Lecture series in Bioinformatics and Computational Biology, Iowa State University, April 10, 2014
174 "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
173 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
The Office of Interdisciplinary Graduate Programs, Spring Reception Poster Presentation
172 Computational modeling of macromolecular structures, Juan Esquivel-Rodriguez, Interdisciplinary graduate program, LWSN3102, Purdue, March 5, 2014
171 2nd Zing Protein and RNA Structure Prediction Conference, Cancun, Mexico, Dec. 1-5, 2013
2nd Zing Protein and RNA Structure Prediction Conference
170 Beckman Institute, Univ. Illinois at Urbana-Chanpain, Oct 28, 2013
169 Daisuke Kihara, Department seminar, Dept. of Bilogical Sciences, Purdue University, Oct 2, 2013
168 "Prediction of macromolecular structures of protein interactions", Cold Spring Harbor Asia Conferences on Frontiers in Bioinformatics and Computational Biology , Sep 23-27, 2013
Frontiers in Bioinformatics and Computational Biology
167 University College London, UK Sep 13, 2013
166 2nd ACSL International Summer School, Imperial College London, Sep 8-14, 2013
165 "Unified biomolecular 3D surface matching for proteins, ligands, and interactions", Eli Lilly, seminar at Lilly Grand Rounds, Eli Lilly, Indianapolis, Aug 14, 2013
164 "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
Annual Symposium of the Protein Society
163 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
162 "Machine learning approach for protein structure modeling" Telluride Workshop on "Modeling biomolecular structures, interactions and functions", telluride, CO, July 1-5, 2013
"Modeling biomolecular structures, interactions and functions"
161 "On protein docking prediction", Seoul National University, Chemistry department, Seoul, Korea, 3pm, June 27, 2013
160 "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
159 "Predicting gene function in biological contexts", Seoul National University, Computer Science and Engineering, Seoul, Korea 11am, June 24, 2013
158 "Information flow in biological systems", Tokyo Institute of Technology, Tokyo, Japan, June 21, 2013
157 "Predictions of structures of protein interactions". D. Kihara, Toyota Technological Institute at Chicago, Chicago, IL, May 20, 2013
156 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.
155 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.
154 Predictions of Protein Function, Structures, Dynamics, and Interactions. Bioinformatics and Machine Learning Roundtable, Qatar Computing Res. Institute, Doha, Qatar, March 19-20, 2013.
153 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.
152 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.
151 Macromolecular Structure Modeling and Electron Microscopy Fitting Using 3D Zernike Descriptors. Highlights Track, ISCB-Asia/SCCG 2012, Shenzhen, China, Dec. 17-19, 2012.
150 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
149 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.
148 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
147 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.
146 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
145 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
144 Invited talk by D. Kihara at Telluride Meeting on Coarse-grained modeling of structure and dynamics of biomacromolecules, Telluride, Colorado, July 23-27, 2012
Coarse-grained modeling of structure and dynamics of biomacromolecules
143 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
142 Invited talk by D. Kihara at Telluride Meeting on Protein folding and Dynamics: From experiment to theory, Telluride, Colorado, June 17-21, 2012
Protein folding and Dynamics: From experiment to theory
141 "Predicting binding ligand and protein docking using surface shape". D. Kihara, Graduate School of Information Science, Tohoku University, Sendai, Japan. May 30, 2012
140 "Preditions of structures of protein interactions". D. Kihara, Bioinformatics Seminar series at Institute of Chemical Research, Kyoto University , Uji, Kyoto, Japan. May 28, 2012
Bioinformatics Seminar series at Institute of Chemical Research, Kyoto University
139 "Systems Level Gene Function Prediction for Assessing Outcome of SNPs", D. Kihara, Chung-Ang University, Seoul, Korea, May 25, 2012
138 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
Great Lakes Bioinformatics Conference (GLBIO) 2012
137 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
136 "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
2012 Undergraduate Research and Poster Symposium
135 "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.
134 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
133 "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 .
132 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
Sigma Xi Graduate Student Research Award Competition
131 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
Zing conference, IECA (Internatinal E. coli Alliance) 2011
130 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
Zing conference on Protein and RNA Structure Prediction"
129 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
Ustream video
128 Ph.D. thesis defense, Bin Li, "Geometrical Analysis Of Interaction Sites Of Proteins", Dept. of Computer Science, Purdue University, Nov. 29, 2011.
127 "Next generation structural bioinformatics and gene function prediction", D. Kihara, Biological Scieces Researh Retreat, Swan Lake resort, Plymonth IN, November 5, 2011
126 "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
125 "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
124 Invited Seminar, "Protein surface representation for ligand binding site screening" D. Kihara, Eli Lilly, Indianapolis,October 3, 2011
123 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
122 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
121 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
120 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
119 Invited Seminar,"Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions" D. Kihara, RIKEN, Yokahama, Japan, August 30, 2011
118 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
ICR Bioinformatics Center, 10 Year Anniversary and New Reconstructing Symposium
117 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
116 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)
ISMB, Viena, Austria, July 15-19, 2011
115 "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.
"Modeling Biomolecular Structures, Interactions, and Functions"
114 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"
International PhD Studies program, Faculty of Chemistry, Warsaw University
113 "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
International Institute of Molecular and Cell Biology
112 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
International Conference on Structural Genomics
111 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
Great Lakes Bioinformatics Conference 2011, May 2-4, 2011, Ohio University, Athens, Ohio
110 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)
2011 Undergraduate Research and Poster Symposium
109 "General framework for multiple protein docking" Juan Esquivel-Rodriguez, D. Kihara, 2011 Interdisciplinary Graduate Program Spring Reception, PMU, Purdue University, April 20, 2011
108 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)
107 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)
55st Annual meeting of Biophysical Society
106 "Predicting protein function by surface comparison" by Sael Lee, at Bioinformatics seminar, Statistics on Feb 15, 4:30pm, HORT 117, Purdue.
Bioinformatics seminar
105 "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
104 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
The 21st International Conference on Genome Informatics
103 "Binding ligand prediction using local surface Zernike descriptors". December 15, 2010, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
102 "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
101 "Protein-protein docking prediction: from pairwise docking, docking using docking interface information, and multiple docking". December 14, 2010, Shanghai Jiaotong University, Shanghai, China
100 "Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups". December 13, 2010, Fudan University, Shanghai, China
99 "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
98 "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.
97 Ph.D. thesis defense, Sael Lee, "High throughput screening of global and local protein surfaces.", Dept. of Computer Science, Purdue University, July 16, 2010.
96 "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.
95 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
3DSIG 2010
94 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
93 Invited talk, "Molecular surface representation for protein shape comparison and docking", D. Kihara, Korea Institute for Advanced Study (KIAS), June 30, 2010, Seoul, Korea.
92 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
91 "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.
90 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
89 "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
88 "Exploring applications of suboptimal alignments in threading protein structure prediction" Hao Chen, Ph.D. Thesis defense. Apr. 6, 2pm, Lilly 1-117, Purdue University.
87 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.
86 "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
85 "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
84 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
83 "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
Biophysical Society meeting
82 "Protein surface representation for fast structure search, docking and function prediction", Tokyo Institute of Technology, Dept. of Computer Science, Tokyo, Japan, Dec 28, 2009
81 "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
80 "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
CAPRI Critical Assessment of Predicted Interactions 4th Evaluation Meeting
79 "Protein Structure Bioinformatics for Predicting Structure, Docking, and Function" Univ. Cincinnati, Nov. 5, 2009
78 "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
77 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
76 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.
75 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
American Society for Microbiology
74 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"
73 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
72 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"
The 21st Undergraduate Research Conference at Butler University
71 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.
70 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"
SIAM@Purdue Student Conference 09
69 Ph.D. thesis defense, Troy Hawkins, Dept. of Biological Sciences, Purdue University, October 6, 2008
68 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
Biophysical Society 53nd Annual Meeting
67 Seminar at the Biochemistry seminar series "Annotating protein structures by surface shape comparison" by D. Kihara, Feb 27th, 11:30-12:15, WTHR 201
66 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.
65 Guest lecture on our research projects in protein bioinformatics at CS 197 Honors Seminar, Feb 16, 9:30-10:20, LWSN B134.
64 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
e-Bioinformatics Workshop IEEE e-Science '08
63 Daisuke Kihara, Depatmental Seminar at Biological Sciences, Purdue Univesity, "Informatics approaches for studying protein sequence, structure, and function in omics era, Oct. 15, 2008
62 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
61 "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.
60 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,
59 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.
58 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.
AFP/Biosapiens 2008
57 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.
56 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"
55 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
54 Poster presentations at Biophysical Society 52nd Annual Meeting February 2-6, 2008, Long Beach, CA
Biophysical Society 52nd Annual Meeting
53 (3250-Pos/B553)Predicting the error of template-based protein structure modeling by suboptimal alignment stability, by Hao Chen & D. Kihara
52 (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
51 Invited talk "Template-based protein structure prediction and beyond" at Korea Institute of Science and Technology Information (KISTI), December 26, 2007, Daejeon, Korea
Korea Institute of Science and Technology Information (KISTI)
50 Invited talk "Computational protein structure and function prediction" at Chung-Ang University, December 27, 2007, Seoul, Korea
49 7th KIAS-Soongsil Conference, October 4-6, 2007, Soongsil Univ., Seoul, Korea, "Protein function prediction for proteomics era (invited talk) "
48 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
47 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
46 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)
Biomedical Engineering Society Annual Meeting
45 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)
The 21st Symposium of the Protein Society
44 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.
ISMB 2007
43 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"
Indy '07: Indy Regional Bioinformatics Conference
42 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
Interface 2007: the 39th Symposium on the interface of statistics, computing science, and applications
41 " Protein function and structure prediction for proteomics analyses " Invisted talk at Indiana University, Informatics Department, May 3, 2007, Bloomington, IN
40 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
39 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
2007 Undergraduate Research and Poster Symposium
38 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
37 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
36 One-day course on bioinformatics , Graduate program, Kansai Medical University, Osaka, Japan, December 25, 2006, "Bioinformatics: Introduction and advanced topics", Daisuke Kihara
35 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
34 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
Critical Assessment of Techniques for Protein Structure Prediction (CASP7)
33 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)
BMES2006: (Biomedical Engineering Society Annual Meeting 2006) "Systems Biology and Bioinformatics" Track
32 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)
31 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)
The Second Automated Function Prediction Meeting
30 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)
29 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
TeraGrid '06
28 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
The Third Annual Indiana Bioinformatics Conference
27 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
26 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
25 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)
2006 Sigma Xi Graduate Studnet ReserachPoster Presentation
24 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
23 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),
The 16th International Conference on Genome Informatics
22 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)
International Symposium "From Genomics to Chemical Genomics: 10th Anniversary of KEGG
21 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)
International Symposium on Frontiers of Computational Science 2005
20 Structural Biology Seminar, November 16, 2005, Department of Biological Sciences, Purdue University, "Protein function prediction methods beyond BLAST search", Daisuke Kihara
19 Computer Research Institute Seminar, October 19, 2005, Computing Reserach Institute, Purdue University, "Protein function prediction in Structural Genomics Era", Kihara
Computer Research Institute Seminar
18 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
17 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)
16 PULSe Retreat, August 20, 2005, John S. Wright Forestry Center at Martell Forest, "Computational Function Prediction", Troy Hawkins, Stan Luban, Daisuke Kihara
15 Biology Department New Graduate Students Orientation, August 12, 2005, Lilly Hall of Life Sciences, Purdue University, "Bioinformatics Research in Kihara Lab", Daisuke Kihara
14 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
13 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
12 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
ISMB oral presentation program
11 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
10 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
9 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
Department of Computer Science Purdue University news article
8 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
7 Biochemistry Division Seminar, April 1 2005, "Toward a better template-based protein structure prediction", Daisuke Kihara
6 Biology Honors Research (BIOL 497) Presentation, March 31 2005 , Lilly Hall of Life Sciences, Purdue University, Stan Luban
5 PULSe Graduate Students Recruitment, March 5 2005, Hansen Hall, Purdue University, "Protein Sequence-Structure Alignment with a Reliability Measure", Hao Chen
4 CS department Graduate Student Recruitment, March 5 2005, Computer Science Building, Purdue University, "Bioinformatics Research in Kihara group", Daisuke Kihara
3 Biology Graduate Students Recruitment, February 26 2005,"Research in Kihara Bioinformatics Lab!", Troy Hawkins
2 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
1 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