Publications

# Year Publication Name Relevant Links
Punyatoya Panda, Swagarika J. Giri, Louis Sherman, Daisuke Kihara, & Uma K. Aryal, Proteomic analysis of unicellular cyanobacterium Crocosphaera subtropica ATCC 51142 under extended light or dark growth, bioRxiv, (2024) PDF Abstract
Punyatoya Panda, Swagarika J. Giri, Louis A. Sherman, Daisuke Kihara, & Uma K. Aryal, Proteomic changes orchestrate metabolic acclimation of a unicellular diazotrophic cyanobacterium during light-dark cycle and nitrogen fixation states, bioRxiv, (2024) PDF Abstract
Jacob Verburgt, Zicong Zhang, & Daisuke Kihara, AlphaFold Model Quality Self-Assessment Improvement Via Deep Graph Learning, bioRxiv, (2024) PDF
Farhanaz Farheen, Bradley K. Broyles, Yuanyuan Zhang, Nabil Ibtehaz, Alexandre M. Erkine, & Daisuke Kihara, Predicting transcriptional activation domain function using Graph Neural Networks, bioRxiv, (2024) PDF Abstract
Woong-Hee Shin & Daisuke Kihara, PL-PatchSurfer3: Improved Structure-Based Virtual Screening for Structure Variation Using 3D Zernike Descriptors, bioRxiv, (2024) PDF Abstract
Tunde Aderinwale, Rashidedin Jahandideh, Zicong Zhang, Bowen Zhao, Yi Xiong, & Daisuke Kihara, AFM-RL: Large Protein Complex Docking Using AlphaFold-Multimer and Reinforcement Learning, bioRxiv, (2024) PDF Abstract
Zicong Zhang, Jacob Verburgt, Yuki Kagaya, Charles Christoffer, & Daisuke Kihara, Improved Peptide Docking with Privileged Knowledge Distillation using Deep Learning, bioRxiv, (2023) PDF Abstract
Yuanyuan Zhang, Zicong Zhang, Yuki Kagaya, Genki Terashi, Bowen Zhao, Yi Xiong, & Daisuke Kihara, Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints, bioRxiv, (2023) PDF Abstract
Yuki Kagaya, Zicong Zhang, Nabil Ibtehaz, Xiao Wang, Tsukasa Nakamura, David Huang, & Daisuke Kihara, NuFold: A Novel Tertiary RNA Structure Prediction Method Using Deep Learning with Flexible Nucleobase Center Representation, bioRxiv, (2023) PDF Abstract
262 2025 Pranav Punuru, Anika Jain, & Daisuke Kihara, Secondary Structure Detection and Structure Modeling for Cryo-EM, Methods in Molecular Biology, 2870: 341-355, (2025) PDF Abstract
261 2024 Xiao Wang, Han Zhu, Genki Terashi, Manav Taluja, & Daisuke Kihara, DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model, Nature Methods, online ahead (2024) PDF Abstract
260 2024 Javad Baghirov, Xiao Wang, Genki Terashi, Shu Li, & Daisuke Kihara, Computational Methods for Bimolecular Structure Modeling for Cryo-EM, Cryo-EM 2024, Cryo-Electron Microscopy in Structural Biology, Krishnarao Appasani (ed.) , Chapter 9, pp. 131-141, Taylor & Francis, (2024) PDF Abstract
259 2024 Taher Yacoub, Nika Zarubina, Camille Depenveiller, Hoang-Phuc Nguyen, Vinh-Toan Vong, Minh-Triet Tran, Yuki Kagaya, Tsukasa Nakamura, Daisuke Kihara, Florent Langenfeld, & Matthieu Montes, SHREC2024: Non-rigid Complementary Shapes Retrieval in Protein-protein Interactions, Eurographics Workshop on 3D Object Retrieval. (2024) PDF Abstract
258 2024 Charles W. Christoffer, Tsukasa Nakamura, Xusi Han, Woong-Hee Shin, Genki Terashi, Lyman Monroe, Lukasz Kurgan, & Daisuke Kihara, Study of the Variability of the Native Protein Structure, Encyclopedia of Bioinformatics and Computational Biology, 2nd Edition, in press (2024)
257 2024 Andy Lee, Benjamin N Daniels, William Hemstrom, Cataixa López, Yuki Kagaya, Daisuke Kihara, Jean M Davidson, Robert J Toonen, Crow White, & Mark R Christie, Genetic adaptation despite high gene flow in a range-expanding population, Molecular Ecology, e17511, (2024) PDF Abstract
256 2024 Fadi Bou-Abdallah, Jeremie Fish, Genki Terashi, Yuanyuan Zhang, Daisuke Kihara, & Paolo Arosio, Unveiling the stochastic nature of human heteropolymer ferritin self-assembly mechanism, Protein Science, 33: e5104 (2024) PDF Abstract
255 2024 Yuanyuan Zhang, Xiao Wang, Zicong Zhang, Yunhan Huang, & Daisuke Kihara, Assessment of Protein-Protein Docking Models Using Deep Learning, Methods in Molecular Biology, 2780: 149-162 (2024) PDF Abstract
254 2024 Catherine L Lawson, ,,, Daisuke Kihara, ,,, Sai R Maddhuri Venkata Subramaniya, ,,, Daipayan Sarkar, ,,, Genki Terashi, ,,, Jacob Verburgt, Xiao Wang, ,,, & Wah Chiu (81 authors), Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge, Nature Methods, 21: 1340-1348, (2024) PDF Abstract
253 2024 Swati Jain, ,,, Woong-Hee Shin, ,,, Daisuke Kihara, ,,, & Venigalla B. Rao (18 Authors), A Remarkable Genetic Shift in a Transmitted/Founder Virus Broadens Antibody Responses Against HIV-1, eLife, 13:RP92379 (2024) PDF Abstract
252 2024 Swagarika Jaharlal Giri, Nabil Ibtehaz, & Daisuke Kihara, GO2Sum: Generating Human Readable Functional Summary of Proteins from GO Terms, npj Systems Biology and Applications, 10: 29 (2024) PDF Abstract
251 2024 Yury V Bukhman, ,,, Aashish Jain, Daisuke Kihara, ,,, & Ron Stewart (36 Authors) , A high-quality blue whale genome, segmental duplications, and historical demography, Molecular Biology and Evolution, 41: msae036 (2024) PDF Abstract
250 2024 Charles Christoffer, Kannan Harini, Gupta Archit, & Daisuke Kihara, Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints, Journal of Molecular Biology, 436: 168486 (2024) PDF Abstract
249 2024 Yury V. Bukhman, ,,, Swagarika Jaharlal Giri, ,,, Daisuke Kihara, ,,, & Ron Stewart (26 authors), Chromosome level genome assembly of the Etruscan shrew Suncus etruscus, Scientific Data, 11: 176 (2024) PDF Abstract
--- 2024 Daisuke Kihara, Editorial: Expert opinions in protein bioinformatics: 2022, Frontiers in Bioinformatics, 3: 1338560 (2024) PDF Abstract
248 2024 Genki Terashi, Xiao Wang, Devashish Prasad, Tsukasa Nakamura, & Daisuke Kihara, DeepMainmast: Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction, Nature Methods, 21: 122-131 (2024) PDF Abstract
247 2024 Jacob Verburgt, Anika Jain, & Daisuke Kihara, Recent Deep Learning Applications to Structure-Based Drug Design, Methods in Molecular Biology, 2714: 215-234 (2024) PDF Abstract
246 2023 Nabil Ibtehaz, Yuki Kagaya, & Daisuke Kihara, Domain-PFP allows protein function prediction using function-aware domain embedding representations, Communications Biology, 6: 1103 (2023) PDF Abstract
245 2023 M.F. Lensink, ,,, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, ,,, Kihara D, ,,, & S.J. Wodak (113 authors), Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment, Proteins, 91: 1658-1683 (2023) PDF Abstract
244 2023 Genki Terashi & Daisuke Kihara, Biomolecular structure model evaluation and modeling for cryo-EM maps, JSBi Bioinformatics Review, 4: 91-103 (in Japanese) (2023) PDF Abstract
243 2023 Nabil Ibtehaz & Daisuke Kihara, ACC-UNet: A Completely Convolutional UNet Model for the 2020s, Medical Image Computing and Computer Assisted Intervention (MICCAI 2023) Vancouver, Canada (2023) PDF Abstract
242 2023 Xiao Wang, Genki Terashi, & Daisuke Kihara, CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning, Nature Methods, 20: 1739-1747 (2023) PDF Abstract
241 2023 Daisuke Kihara, Tools for effective use of the Alphafold DB, Jikken Igaku (Experimental Medicine), 41: 2575-2579 (in Japanese) (2023)
240 2023 Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & Daisuke Kihara , Enhancing Cryo-EM Maps With 3D Deep Generative Networks For Assisting Protein Structure Modeling, Bioinformatics, 39: btad494 (2023) PDF Abstract
239 2023 Kannan Harini, Charles Christoffer, M Michael Gromiha, & Daisuke Kihara, Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server, Methods in Molecular Biology, 2690: 355-373 (2023) PDF Abstract
238 2023 Hugo Schweke, ,,, Xiao Wang, Genki Terashi, Daipayan Sarkar, Charles Christoffer, Tunde Aderinwale, Jacob Verburgt, Daisuke Kihara, ,,, Emmanuel D. Levy & Shoshana J. Wodak (56 authors), Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study, Proteomics, 23: e2200323 (2023) PDF Abstract
237 2023 Tsukasa Nakamura, Xiao Wang, Genki Terashi, & Daisuke Kihara, DAQ-Score Database: assessment of map-model compatibility for protein structure models from cryo-EM maps, Nature Methods, 20: 775-776 (2023) PDF Abstract
236 2023 Jennifer J. Lee, Swetha Ramadesikan, Adrianna F. Black, Charles Christoffer, Andres F. Pacheco Pacheco, Sneha Subramanian, Claudia B. Hanna, Gillian Barth, Cynthia V. Stauffacher, Daisuke Kihara, & Ruben Claudio Aguilar, Heterogeneity in Lowe Syndrome: Mutations Affecting the Phosphatase Domain of OCRL1 Differ in Impact on Enzymatic Activity and Severity of Cellular Phenotypes, Biomolecules, 13: 615 (2023) PDF Abstract
235 2023 K. Harini, Daisuke Kihara, & M. Michael Gromiha, PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features, Methods, 213: 10-17 (2023) PDF Abstract
234 2023 Genki Terashi, & Daisuke Kihara, Recent Advances in Biomolecular Structure Modeling and Validation using Deep Learning, Nihon Kessho Gakkaishi (Journal of the Crystallographic Society of Japan), 65: 3-9 (in Japanese) (2023) PDF Abstract
233 2023 Sushmita Basu, Daisuke Kihara, & Lukasz Kurgan, Computational prediction of disordered binding regions, Computational and Structural Biotechnology Journal, 21: 1487-1497 (2023) PDF Abstract
232 2023 Woong-Hee Shin, Keiko Kumazawa, Kenichiro Imai, Takatsugu Hirokawa, & Daisuke Kihara, Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches, Frontiers in Molecular Biosciences, 10: 1110567 (2023) PDF Abstract
231 2023 Harrison Helmick, Anika Jain, Genki Terashi, Andrea Liceaga, Arun K Bhunia, Daisuke Kihara, & Jozef L Kokini, Bioinformatic Approaches for Characterizing Molecular Structure and Function of Food Proteins, Annual Review of Food Science And Technology, 14: 203-22 (2023) PDF Abstract
230 2023 Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin S Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, & George D Rose, Opinion: Protein folds vs. protein folding: Differing questions, different challenges, PNAS, 120: e2214423119 (2023) PDF Abstract
229 2023 Charles Christoffer, & Daisuke Kihara, Modeling Protein-Nucleic Acid Complexes with Extremely Large Conformational Changes using Flex-LZerD, PROTEOMICS, 23: e2200322 (2023) PDF Abstract
228 2023 Genki Terashi, Xiao Wang, & Daisuke Kihara, Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score, Acta Cryst. D, 79: 10-21 (2023) PDF Abstract
227 2023 Nabil Ibtehaz & Daisuke Kihara, Application of sequence embedding in protein sequence-based Predictions, Machine Learning in Bioinformatics of Protein Sequences: Algorithms, Databases and Resources for Modern Protein Bioinformatics, Lukasz Kurgan (ed.), Chapter 2, pp. 31-55, World Scientific (2023) Abstract
226 2023 Anna T Olek, Phillip S Rushton, Daisuke Kihara, Peter Ciesielski, Uma K Aryal, Zicong Zhang, Cynthia V Stauffacher, Maureen C McCann, & Nicholas C Carpita, Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases, Plant Physiology, 19, 142-160 (2023) PDF Abstract
225 2022 Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M Phillippy, Scott A Swanson, Peng Jiang, Dennis O Clegg, Erich D Jarvis, James A Thomson, Ron Stewart, Mark J P Chaisson, & Yury V Bukhman, A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes, BMC Biology, 20: 245 (2022) PDF Abstract
224 2022 Charles Christoffer & Daisuke Kihara, Domain-Based Protein Docking with Extremely Large Conformational Changes, Journal of Molecular Biology, 434: 167820 (2022) PDF Abstract
223 2022 Genki Terashi, Xiao Wang, Sai Raghavendra Maddhuri Venkata Subramaniya, John J. G. Tesmer, & Daisuke Kihara, Residue-wise local quality estimation for protein models from cryo-EM maps, Nature Methods, 19: 1116-1125 (2022) PDF Abstract
222 2022 Daisuke Kihara, New standard of protein structure prediction, Jikken Igaku (Experimental Medicine), 40: 221-227 (in Japanese) (2022)
221 2022 Tunde Aderinwale, Charles Christoffer, & Daisuke Kihara, RL-MLZerD: Multimeric Protein Docking Using Reinforcement Learning, Frontiers In Molecular Biosciences, 9: 969394 (2022) PDF Abstract
220 2022 Gagliardi L, Raffo A, Fugacci U, Biasotti S, Rocchia W, Huang H, Amor B, Fang Y, Yuanyuan Zhang, Xiao Wang, Charles Christoffer, Daisuke Kihara, Axenopoulos A, Mylonas S, & Daras P, SHREC 2022: Protein-ligand binding site recognition, Computers & Graphics, 107: 20-31 (2022) Abstract
219 2022 Eman Alnabati, Juan E. Esquivel-Rodriguez, Genki Terashi, & Daisuke Kihara, MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field, Frontiers in Molecular Biosciences, 9: 935411 (2022) PDF Abstract
218 2022 Eman Alnabati, Genki Terashi, & Daisuke Kihara, Protein structure modeling for cryo-EM using VESPER and MAINMAST, Current Protocols, 2: e494 (2022) PDF Abstract
217 2022 Xiao Wang, Haoqi Fan, Yuandong Tian, Daisuke Kihara, & Xinlei Chen, On the Importance of Asymmetry for Siamese Representation Learning, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2022: 16570-16579 (2022) PDF Abstract
216 2022 Jacob Verburgt, Zicong Zhang, & Daisuke Kihara, Multi-level analysis of intrinsically disordered protein docking methods, Methods, 204: 55-63 (2022) PDF Abstract
215 2022 Yuki Kagaya, Aashish Jain, Sean Flannery, & Daisuke Kihara, ContactPFP: Protein function prediction using predicted contact information, Frontiers in Bioinformatics, 2: 896295 (2022) PDF Abstract
214 2022 Lyman Monroe, & Daisuke Kihara, Using steered molecular dynamic tension for assessing quality of computational protein structure models, Journal of Computational Chemistry, 43: 1140-1150 (2022) PDF Abstract
213 2022 Tunde Aderinwale, Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh, Yuki Kagaya, & Daisuke Kihara, Real-time structure search and structure classification for AlphaFold protein models, Communications Biology, 5: 316 (2022) PDF Abstract
212 2022 Xiao Wang, M. Kittaka, Yilin He, Yiwei Zhang, Y. Ueki, & Daisuke Kihara, OC_Finder: Osteroclast segmentation, counting, and classification using watershed and deep learning, Frontiers in Bioinformatics, 2: 819570 (2022) PDF Abstract
211 2022 M. Elloumi, M.A.Ahmad, A.H. Samak, A.M. Al-Sharafi, Daisuke Kihara, & A.I. Taloba, Error correction algorithms in non-null aspheric testing next generation sequencing data, Alexandria Engineering Journal, 61: 9819-9829 (2022) PDF Abstract
210 2022 Florent Langenfeld, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Genki Terashi, Xiao Wang, Daisuke Kihara, Halim Benhabiles, Karim Hammoudi, Adnane Cabani, Feryal Windal, Mahmoud Melkemi, Ekpo Otu, Reyer Zwiggelaar, David Hunter, Yonghuai Liu, Léa Sirugue, Huu-Nghia H Nguyen, Tuan-Duy H Nguyen, Vinh-Thuyen Nguyen-Truong, Danh Le, Hai-Dang Nguyen, Minh-Triet Tran, & Matthieu Montès, Surface-based protein domains retrieval methods from a SHREC2021 challenge, Journal of Molecular Graphics & Modelling, 111: 108103 (2022) Abstract
209 2022 Jacob Verburgt, & Daisuke Kihara, Benchmarking of structure refinement methods for protein complex models, Proteins, 90: 83-95 (2022) Abstract
208 2021 I. Gubins, M.L. Chaillet, G.v.d. Schot, M.C. Trueba, R.C. Veltkamp, F. Forster, Xiao Wang, Daisuke Kihara, E. Moebel, N.P. Nguyen, T. White, F. Bunyak, G. Papoulias, S. Gerolymatos, Z. Stavros, E.I. Zacharaki, K. Moustakas, X. Zeng, S. Liu, M. Xu, Y. Wang, C. Chen, X. Cui, & F. Zhang, SHREC 2021: Classification in cryo-electron tomograms, Eurogaphics Workshop on 3D Object Retrieval, doi:10.2312/3dor.20211307, (2021)
--- 2021 Nir Ben-Tal, Daisuke Kihara, & Arun Prasad Pandurangan, Editorial: Computational approaches to study the impact of mutations on disease and drug resistance, Frontiers in Molecular Biosciences, 8: 813552 (2021) PDF Abstract
207 2021 R.S.P. Rao, N. Ahsan, C. Xu, L. Su, Jacob Verburgt, L. Fornelli , Daisuke Kihara, & D. Xu, Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein, Evolutionary Bioinformatics Online, 17: 11769343211064616 (2021) PDF Abstract
206 2021 Kryshtafovych A., Moult J.,, & CASP-COVID paricipants (including Charles Christoffer, Genki Terashi, Daipayan Sarkar, & Daisuke Kihara), Modeling SARS-CoV-2 proteins in the CASP-commons experiment, Proteins, 89: 1987-1996 (2021) PDF Abstract
205 2021 M.F. Lensink, ,, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, ,, & S.J. Wodak (108 authors), Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment, Proteins, 89: 1800-1823 (2021) PDF Abstract
204 2021 M. Shekhar*, Genki Terashi*, C. Gupta, Daipayan Sarkar, G. Debussche, N.J. Sisco, J. Nguyen, A. Mondal, J. Vant, P. Fromme, W.D. Van Horn, E. Tajkhorshid, Daisuke Kihara, K. Dill, A. Perez, & A. Singharoy (*co-first authors), CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps, Matter, 4: 3195-3216 (2021) PDF Abstract
203 2021 B.K. Broyles, A.T. Gutierrez, T.P. Maris, D.A. Coil, T.M. Wagner, Xiao Wang, Daisuke Kihara, C.A. Class, & A.M. Erkine, Activation of gene expression by detergent-like protein domains, iScience, 24: 103017 (2021) PDF Abstract
202 2021 Charles Christoffer, Vijay Bharadwaj, Ryan Luu, & Daisuke Kihara, LZerD protein-protein docking webserver enhanced with de novo structure prediction, Frontiers in Molecular Biosciences, 8: 724947 (2021) PDF Abstract
201 2021 A. Raffo, U. Fugacci, S. Biasotti, W. Rocchia, Y. Liu, E. Otu, R. Zwiggelaar, D. Hunter, E.I. Zacharaki, E. Psatha, D. Laskos, G. Arvanitis, K. Moustakas, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Daisuke Kihara, A. Giachetti, H.-N. Nguyen, T.-D. Nguyen, V.-T. Nguyen-Truong, D. Le-Thanh, H.-D. Ngyuen, & M.-T. Tran, SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties, Computers & Graphics, 99: 1-21 (2021)
200 2021 Takaharu Mori, Genki Terashi, Daisuke Matsuoka, Daisuke Kihara, & Yuji Sugita, Efficient flexible fitting refinement with automatic error fixing for de novo structure modeling from cryo-EM density maps, Journal of Chemical Information And Modeling, 61: 3516-3528 (2021) PDF Abstract
199 2021 Xiao Wang, Sean Flannery, & Daisuke Kihara, Protein docking model evaluation by graph neural networks, Frontiers in Molecular Biosciences, 8: 647915 (2021) PDF Abstract
198 2021 Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, & Daisuke Kihara, LZerD webserver for pairwise and multiple protein-protein docking, Nucleic Acid Research, 49: W359-W365 (2021) PDF Abstract
197 2021 Anwesha Sanyal, Erica A. Zbornik, Ben G. Watson, Charles Christoffer, Jia Ma, Daisuke Kihara, & Seema Mattoo, Kinetic and strutctural parameters governing Fic-mediated adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78, Cell Stress & Chaperones, 26: 639-656 (2021) Abstract
196 2021 Xiao Wang, Eman Alnabati, Tunde W. Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & Daisuke Kihara, Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning, Nature Communications, 12: 2302 (2021) PDF Abstract
195 2021 Nagib Ahsan, R.S.P. Rao, R.S. Wilson, U. Punyamurtula, F. Salvato, M. Petersen, M.K. Ahmed, M.R. Abid, Jacob C. Verburgt, Daisuke Kihara, L. Fornelli, S.B. Foster, B. Ramratnam, Mass spectrometry-based proteomics platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches, PROTEOMICS, 21: e2000279 (2021) Abstract
--- 2021 Daisuke Kihara, Breakthrough in protein structure prediction - Alphafold2, Jikken Igaku (Experimental Medicine), 39: 906-908 (in Japanese) (2021)
194 2021 Xusi Han#, Genki Terashi#, Charles Christoffer, Siyang Chen, & Daisuke Kihara (# co-first authors), VESPER: global and local cryo-EM map alignment using local density vectors, Nature Communications, 12: 2090 (2021) PDF Abstract
193 2021 Aashish Jain, Genki Terashi, Yuki Kagaya, Sai Raghavendra Venkata Maddhuri Subramaniya, Charles Christoffer, & Daisuke Kihara, Analyzing effect of quadraple multiple sequence alignments on deep learning based protein inter-residue distance prediction, Scientific Reports, 11: 7574 (2021) PDF Abstract
192 2021 Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Aashish Jain, Yuki Kagaya, & Daisuke Kihara, Protein contact map refinement for improving protein structure prediction using generative adversarial networks, Bioinformatics, 37: 3168-3174 (2021) Abstract
191 2021 Catherine L. Lawson, ,,, Daisuke Kihara, ,,, Daipayan Sarkar , ,,, Genki Terashi , ,,, Helen M. Berman, & Wah Chiu (54 authors), Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge, Nature Methods, 18: 156-164 (2021) PDF Abstract
190 2021 Swetha Ramadesikan, Lisette Skiba, Jennifer Lee, Kayalviszhi Madhivanan, Daipayan Sarkar, Agustina De La Fuente, Claudia B. Hanna, Genki Terashi, Tony Hazbinpress Daisuke Kihara, & R. Claudio Aguilar, Genotype & phenotype in Lowe syndrome: Specific OCRL1 patient mutations differentially impact cellular phenotypes, Human Mol. Genet., 30: 198-212 (2021) Abstract
189 2021 Xiao Wang, Daisuke Kihara, Jiebo Luo, & Guo-Jun Qi, EnAET: A self-trained framework for semi-supervised learning with ensemble transformations, IEEE Trans Image Process., 30: 1639-1647 (2021) Abstract
188 2021 Ramanathan Karuppasamy, Shanthi Veerappapillai, Sayoni Maiti, Woong-Hee Shin & Daisuke Kihara, Current progress and future perspective of polypharmacology: From the view of non-small cell lung cancer, Seminars in Cancer Biol., 68: 84-91 (2021) Abstract
187 2020 Woong-Hee Shin, Keiko Kumazawa, Kenichiro Imai, Takatsugu Hirokawa, & Daisuke Kihara, Current challenges and opportunities in designing protein-protein interaction targeted drugs, Advances and Applications in Bioinformatics and Chemistry, 13: 11-25 (2020) PDF Abstract
186 2020 Daisuke Kihara, Charles Christoffer, Siyang Chen, Vijay Bharadwaj, & Tunde Aderinwale, LZerD: Software for protein docking modeling, Jikken Igaku (Experimental Medicine), 38: 3271-3276 (in Japanese) (2020)
--- 2020 Daisuke Kihara, Turning points in my career path, Seibutsu Butsuri (Biophysics), (in Japanese), 61: 44-45 (2020) PDF Abstract
185 2020 I. Gubins, M.L. Chaillet, G.v.d. Schot, R.C. Veltkamp, F. Foerster, Y. Hao, X. Wan, X. Cui, F. Zhang, E. Moebel, Xiao Wang, Daisuke Kihara, X. Zeng, M. Xu, N.P. Nguyen, T. White, & F. Bunyak, SHREC2020: Classification in cryo-electron tomograms, Computers & Graphics, 91: 279-289 (2020) Abstract
184 2020 F. Langenfeld, Y. Peng, Y.-K. Lai, P.L. Rosin, Tunde Aderinwale, Genki Terashi, Charles Christoffer, Daisuke Kihara, H. Benhabiles, K. Hammoudi, A. Cabani, F. Windal, M. Melkemi, A. Giachetti, S. Mylonas, A. Axenopoulos, P. Daras, E. Otu, R. Zwiggelaar, D. Hunter, Y. Liu, & M. Montes, SHREC2020: Multi-domain protein shape retrieval challenge, Computers & Graphics, 91: 189-198 (2020) Abstract
183 2020 Genki Terashi, Yuhong Zha, & Daisuke Kihara, Protein structure modeling from cryo-EMmap using MAINMAST and MAINMAST-GUI Plugin, Methods in Mol. Biol., 2165: 317-336 (2020) Abstract
182 2020 Charles Christoffer & Daisuke Kihara, IDP-LZerD: Software for modeling disordered protein interactions, Methods Mol. Biol., 2165: 231-244 (2020) Abstract
181 2020 Tunde Aderinwale, Charles W. Christoffer, Daipayan Sarkar, Eman Alnabati, & Daisuke Kihara, Computational structure modeling for diverse categories of macromolecular interactions, Curr. Opin. Struct. Biol., 64: 1-8 (2020) Abstract
180 2020 Brenda Gonzalez, Lyman Monroe, Kunpeng Li, Rui Yan, Elena Wright, Thomas Walter, Daisuke Kihara, Susan T. Weintraub, Julie A Thomas, Philip Serwer, & Wen Jiang, Phage G structure at 6.1 A resolution, condensed DNA, and host identity revision to a Lysinibacillus, J. Mol. Biol., 432: 4139-4153 (2020) Abstract
179 2020 Genki Terashi, Yuki Kagaya, & Daisuke Kihara, MAINMASTseg: Automated map segmentation method for cryo-EM density with symmetry, J. Chem. Inf. Model., 60: 2634-2643 (2020) Abstract
178 2020 Daisuke Kihara, Trends in software developments of biomolecular structural modeling and prediction, Jikken Igaku (Experimental Medicine), 38: 866-871 (in Japanese) (2020)
177 2020 Tuan Lai, Quan Huang Tran, Trung Bui, & Daisuke Kihara, A simple but effective BERT model for dialog state tracking on resource-limited systems, IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 8034-8038 (2020) PDF Abstract
176 2020 Genki Terashi, Charles Christoffer, & Daisuke Kihara, Path-LZerD: Predicting assembly order of multimeric protein complexes, Methods in Mol. Biol., 2074: 95-112 (2020) Abstract
175 2020 Genki Terashi, Sai Raghavendra Maddhuri Venkata Subramaniya & Daisuke Kihara, Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning, Jikken Igaku (Experimental Medicine), 38: 82-86 (in Japanese) (2020)
174 2020 Julian S. Deville, Daisuke Kihara, & Atilla Sit, 2DKD: A toolkit for content-based local image search, Source Code for Biology and Medicine, 15:1 (2020) PDF Abstract
173 2020 Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, & Daisuke Kihara, Protein docking model evaluation by 3D convolutional neural networks, Bioinformatics, 36: 2113-2118 (2020) Abstract
172 2020 Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Lenna Peterson, Jacob Verburgt, & Daisuke Kihara, Performance and enhancement of the LZerD protein asssembly pipeline in CAPRI 38-46, Proteins: Structure, Function, and Bioinformatics, 88: 948-961 (2020) Abstract
171 2019 Eman Alnabati & Daisuke Kihara, Advances in structure modeling methods in cryo-electon microscopy maps, Molecules, 25: 82 (2019) PDF Abstract
170 2019 Manuel Zumbado-Corrales, Luis Castillo-Valverde, Jose Salas-Bonilla, Julio Viquez-Murillo, Daisuke Kihara, & Juan Esquivel-Rodriguez, Matching of EM map segments to structurally-relevant Bio-molecular regions, Latin American High Performance Computing Conference, 464-478 (2019) PDF Abstract
169 2019 Chiba S., ,,, Woong-Hee Shin, Daisuke Kihara,,, & Sekijima M., A prospective compound screening contest identified broader inhibitors for Sirtuin 1, Scientific Reports, 9: 19585 (2019) PDF Abstract
168 2019 Aashish Jain & Daisuke Kihara, NNTox: Gene ontology-based protein toxicity prediction using neural network, Scientific Reports, 9: 17923 (2019) PDF Abstract
167 2019 Mark F. Lensink,,, Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Daisuke Kihara ,,,, & Shoshana J Wodak, Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment, Proteins: Structure, Function, and Bioinformatics, 87: 1200-1221 (2019) PDF Abstract
166 2019 Naihui Zhou,,, Aashish Jain,,,, Daisuke Kihara, ,,, Predrag Radivojac, & Iddo Friedberg, The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens, Genome Biology, 20: 244 (2019) PDF Abstract
165 2019 Woong-Hee Shin, & Daisuke Kihara, Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-ParchSurfer2.0, J. Computer-Aided Molecular Design, 33: 1083-1094 (2019) PDF Abstract
164 2019 Tuan Lai, Quan Huang Tran, Trung Bui, & Daisuke Kihara, A gated self-attention memory network for answer selection, The 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing, 5953–5959 (2019) PDF Abstract
163 2019 Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, & Daisuke Kihara, Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning, Nature Methods, 16: 911-917 (2019) PDF Abstract
162 2019 Ramanathan Karuppaswamy, Sayoni V. Shanthi, Woong-Hee Shin & Daisuke Kihara, Implementationof Pharmacophore-based 3D QSAR model and scafford analysis in order to excavate pristine ALK inhibitors, Medicinal Chemistry Research, 28: 1726-1739 (2019) PDF Abstract
161 2019 Ziyun Ding & Daisuke Kihara, Computational identification of protein-protein interactions in model plan proteomes, Scientific Reports, 9: 8740 (2019) PDF Abstract
160 2019 Atilla Sit, Woong-Hee Shin, & Daisuke Kihara, Three-dimensional Krawtchouk descriptors for protein local surface shape comparison, Pattern Recognition, 93: 534-545 (2019) PDF Abstract
159 2019 Ilja Gubins, Gijs van der Shot, Remo C. Veltkamp, Frierich Foerster, Xuefeng Du, Xiangrui Zeng, Zhenxi zhu, Lufan Chang, Min Xu, Emmanuel Moebel, Tuan M. Lai, Xusi Han, Genki Terashi, Daisuke Kihara, Benjamin A. Himes, Xiaohua Wan, Jingrong Zhang, Shan Gao, Yu Hao, Zhilong Lv, Zhidong, Yang, Zijun Ding, Xuefeng Cui, & Fa Zhang, SHREC'19 Track: Classification in cryo-electron tomograms, 12th EG Workshop 3D Object Retrieval 2019, (2019) PDF Abstract
158 2019 Florent Langenfeld, Apostolos Axenopoulos, Halim Benhabiles, Petros Daras, Andrea Giachetti, Xusi Han, Karim Hammoudi, Daisuke Kihara, Tuan M. Lai , Mahmoud Melkemi, Stelios K. Mylonas, Genki Terashi , Yufan Wang, Feryal Windal, & Matthieu Montes, SHREC'19 Protein shape retrieval contest, 12th EG Workshop 3D Object Retrieval 2019, (2019) PDF Abstract
157 2019 Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, & Daisuke Kihara, A global map of the protein shape universe, PloS Computational Biology, 15(4):e1006969 (2019) PDF Abstract
156 2019 Melanie L'Enfant, Pricillia Kutudila, Catherine Rayon, Jean-Marc Domon, Woong-Hee Shin, Daisuke Kihara, Anne Wadouachi, Jerome Pelloux, Gwladys Pourceau, & Corinne Pau-Roblot, Lactose derivatives as potential inhibitors of pectin methylesterases, Int. J. Biological Macromolecules, 132: 1140-1146 (2019) PDF Abstract
155 2019 Mauricio Macossay-Casillo, Giulio Marvelli, Mainak Guharoy, Aashish Jain, Daisuke Kihara, Peter Tompa, & Shoshana Wodak, The balancing act of intrincically disordered proteins: enabling functional diversity while minimizing promiscuity, J. Mol. Biol., 431: 1650-1670 (2019) PDF Abstract
154 2019 Woong-Hee Shin & Daisuke Kihara, 55 years of the Rossmann fold, Methods in Mol. Biol., 1958: 1-13 (2019) PDF Abstract
153 2019 Charles W. Christoffer & Daisuke Kihara, Modeling protein-protein interactions with intrisically disordered proteins, Intrinsically Disordered Proteins, Nicola Salvi (ed.), pp. 189-206 Elsevier (2019) PDF Abstract
152 2019 Xusi Han, Woong-Hee Shin, Charles W. Christoffer, Genki Terashi, Lyman Monroe, & Daisuke Kihara, Study of the variability of the native protein structure, Encyclopedia of Bioinformatics and Computational Biology, 3: 606-619 (2019) PDF Abstract
151 2019 Ishita K. Khan, Aashish Jain, Reda Rawi, Halima Bensmail, & Daisuke Kihara, Prediction of protein group function by iterative classification on functional relevance network, Bioinformatics, 35: 1388-1394 (2019) PDF Abstract
150 2019 Aashish Jain & Daisuke Kihara, Phylo-PFP: Improved automated protein function prediction using phylogenetic distance of distantly related sequences, Bioinformatics, 35: 753-759 (2019) PDF Abstract
149 2019 Yi Xiong, Yanhua Qiao, Daisuke Kihara, Hui-Yuan Zhang, Xiaolei Zhu, & Dong-Qing Wei, Survery of machine learning techniques for prediction of the isoform specificity of cytochrome P450 substrates, Current Drug Metabolism, 20: 229-235 (2019) PDF Abstract
148 2018 Genki Terashi, & Daisuke Kihara, Protein tertiary structure modeling from cryo-EM density maps by tree graph optimization, Jikken Igaku (Experimental Medicine), 36: 2767-2770 (in Japanese) (2018)
147 2018 Aashish Jain, Hareesh Gali, & Daisuke Kihara, Identification of moonlighting proteins in genomes using text mining techniques, Proteomics, 18: e1800083 (2018) PDF Abstract
146 2018 Uma K. Aryal*, Ziyun Ding*,Victoria Hedrick, Tiago Jose Paschoal Sobreira, Daisuke Kihara, & Louis A. Sherman (* co-first authors), Analysis of protein complexes in the unicellular cyanobacterium Cyanothece ATCC 51142, J. Proteome Research, 17: 3628-3643 (2018) PDF Abstract
145 2018 Genki Terashi & Daisuke Kihara, De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge, J. Str. Biol., 204: 351-359 (2018) PDF Abstract
144 2018 Ziyun Ding & Daisuke Kihara, Recent computational methods for predicting protein-protein interactions using various protein features, Current Protocols in Protein Science, 93: e62 (2018) PDF Abstract
143 2018 Genki Terashi & Daisuke Kihara, De novo main-chain modeling for EM maps using MAINMAST, Nature Communications, 9: 1618 (2018) PDF Abstract
142 2018 Lenna X. Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Wooong-Hee Shin, & Daisuke Kihara, Modeling the assembly order of multimeric heteroprotein complexes, PLoS Comput. Biol., 14: e1005937 (2018) PDF Abstract
141 2018 Ziyun Ding, Qing Wei, & Daisuke Kihara, Computing and visualizing gene function similarity and coherence with NaviGO, Methods in Mol. Biol., 1807: 113-130 (2018) PDF Abstract
140 2018 Woong-Hee Shin & Daisuke Kihara, Virtual ligand screening using PL-PatchSurfer2, a molecular surface-based protein-ligand docking method, Methods in Mol. Biol., 1762: 105-121 (2018) PDF Abstract
139 2018 Lenna X. Peterson, Woong-Hee Shin, Hyungrae Kim, & Daisuke Kihara, Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions, Proteins: Structure, Function, and Bioinformatics, 86 (Suppl 1): 311-320 (2018) PDF Abstract
138 2018 Genki Terashi & Daisuke Kihara, Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent, Proteins: Structure, Function, and Bioinformatics, 86 (Supppl 1): 189-201 (2018) Abstract
137 2018 Satwica Yerneni, Ishita K Khan, Qing Wei, & Daisuke Kihara, IAS: Interaction specific GO term associations for predicting protein-protein interaction networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15: 1247-1258 (2018) PDF Abstract
136 2017 S. Chiba, T. Ishida, K. Ikeda, M. Mochizuki, R. Teramoto, Y.H. Taguchi, M. Iwadate, H. Umeyama, C. Ramakrishnan, A.M. Thangakani, D. Velmurugan, M.M. Gromiha, T.Okuno, K. Kato, S. Minami, G. Chikenji, S.D. Suzuki, K. Yanagisawa, Woong-Hee Shin, Daisuke Kihara, K.Z. Yamamoto, Y. Moriwaki, N. Yasuo, R. Yoshino, S. Zozulya, P. Borysko, R. Stavniichuk, T. Honma, T. Hirokawa, Y. Akiyama, & M. Sekijima, An interative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes, Scientific Reports, 7: 12038 (2017) PDF Abstract
135 2017 Xusi Han, Qing Wei, & Daisuke Kihara, Protein 3D structure and electron microscopy map retrieval using 3D-SURFER2.0 and EM-SURFER, Current Protocols, 60: 3.14.1-3.14.15 (2017) PDF Abstract
134 2017 Woong-Hee Shin*, Charles Christoffer*, & Daisuke Kihara (*co-first author), In silico structure-based approaches to discover protein-protein interaction targeting drugs, Methods, 131: 22-32 (2017) PDF Abstract
133 2017 Ishita K. Khan, Mansurul Bhuiyan, & Daisuke Kihara, DextMP: deep dive into text for predicting moonlighting proteins, Bioinformatics, 33: i83-i91 (2017), Presented at ISMB2017 PDF Abstract
132 2017 Na Song, Daniela Craciun, Charles W. Christoffer, Xusi Han, Daisuke Kihara, Guillaume Levieux, Matthieu Montes, Hong Qin, Pranjal Sahu, Genki Terashi, & Haiguang Liu, SHREC'17 Track: Protein shape retrieval, Eurographics Workshop on 3D Object Retrieval, I. Pratikakis, F. Dupont, & M. Ovsjanikov (Eds.) (2017) PDF Abstract
131 2017 Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, & Daisuke Kihara, Modeling disordered protein interactions from biophysical principles, PLoS Computational Biol., 13: e1005485 (2017) PDF Abstract
130 2017 Sayoni Das, Ishita Khan, Daisuke Kihara, & Christine Orengo, Exploring structure-function relationships in moonlighting proteins, Moonlighting Proteins: Novel Virulence Factors in Bacterial Infections, B. Henderson (ed.) Chapter 2, pp. 21-44, Wiley-Blackwell (2017) PDF Abstract
129 2017 Qing Wei, Ishita Khan, Ziyun Ding, Satwica Yerneni, & Daisuke Kihara, NaviGO: Interactive tool for visualization and funtional similarity and coherence analysis with gene ontology, BMC Bioinformatics, 18: 177 (2017) PDF Abstract
128 2017 Lyman Monroe*, Genki Terashi*, & Daisuke Kihara (* co-first authors), Variability of protein structure models from electron microscopy, Structure, 25: 592-602 (2017) PDF Abstract
127 2017 Woong-Hee Shin, Xuejiao Kang, Jian Zhang, & Daisuke Kihara, Prediction of local quality of protein structure models considering spatial neighbors in graphical models, Scientific Reports, 7: 40629 (2017) PDF Abstract
126 2017 Qing Wei, David La, & Daisuke Kihara, BindML/BindML+: Detecting protein-protein interface propensity from amino acid substitution patterns, Methods in Molecular Biology, 1529: 279-289 (2017) PDF Abstract
125 2017 Lenna X. Peterson, Michal Jamroz, Andrzej Kolinski, & Daisuke Kihara, Predicting real-valued protein residue fluctuation using FlexPred, Methods in Mol. Biol., 1484: 175-186 (2017) PDF Abstract
124 2017 Lingfei Zeng*, Woong-Hee Shin*, Xiaolei Zhu, Sung Hoon Park, Chiwook Park, W. Andy Tao, & Daisuke Kihara (* equal contribution), Dicovery of NAD-binding proteins inthe E.coli proteome using combined energetic-based and structural-bioinformatics-based approach, J. Proteome Res., 16: 470-480 (2017) PDF Abstract
123 2017 Lenna X. Peterson, Hyungrae Kim, Juan Esquivel-Rodriguez, Amitava Roy, Xusi Han, Woong-Hee Shin, Jian Zhang, Genki Terashi, Matt Lee, & Daisuke Kihara, Human and server docking prediction for CAPRI Round 30-35 using LZerD with combined scoring functions, Proteins: Structure Function, and Bioinformatics, 85: 513-527 (2017) PDF Abstract
122 2017 Ishita K. Khan, Joshua McGraw, & Daisuke Kihara, MPFit: Computational tool for predicting moonlighting proteins, Methods in Mol. Biol., 1611:45-47 (2017) PDF Abstract
121 2017 Qing Wei, Joshua McGraw, Ishita K. Khan, & Daisuke Kihara, Using PFP and ESG protein function prediction webservers, Methods in Mol. Biol., 1611: 1-14 (2017) PDF Abstract
120 2016 Woong-Hee Shin, Charles Christoffer, Jibo Wang, & Daisuke Kihara, PL-PatchSurfer2: Improved local surface matching-based virtual screening method that is tolerant to target and ligand structure variation, J. Chem. Inf. Model, 56: 1676-1691 (2016) PDF Abstract
119 2016 Meghana Chitale, Ishita K. Khan, & Daisuke Kihara, Missing gene identification using functional coherence scores, Scientific Reports, 6: 31725 (2016) PDF Abstract
118 2016 Abram Magner, Daisuke Kihara, & Wojciech Szpankowski, A study of the Boltzmann sequence-structure channel, Proceedings of the IEEE, 105: 286-306 (2016) PDF
--- 2016 Abram Magner, Daisuke Kihara, & Wojciech Szpankowski, The Boltzmann sequence-structure channel, 2016 IEEE International Symposium on Information Theory (ISIT 2016), 255-259 (2016) PDF
117 2016 Yuxiang Jian,,,, Samuel Chapman, Dukka BKC, Ishita K Khan, Daisuke Kihara,,,, Iddo Friedberg, & Predrag Radivojac (147 authors), An expanded evaluation of protein function prediction methods shows an improvement in accuracy, Genome Biology, 17: 184 (2016) PDF Abstract
116 2016 Laura Kingsley, Juan Esquivel-Rodriguez, Ying Yang, Daisuke Kihara, Markus Lill, Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations, J. Comp. Chem., 37: 1861-1865 (2016) PDF Abstract
115 2016 Michal Jamroz, Andrzej Kolinski, & Daisuke Kihara, Ensemble-based evaluation for protein structure models, Bioinformatics, 32: i314-i321 (2016) Presented at ISMB 2016 PDF Abstract
114 2016 Ishita K. Khan & Daisuke Kihara, Genome-scale prediction of moonlighting proteins using diverse protein association information, Bioinformatics, 32: 2281-2288 (2016) PDF Abstract
113 2016 Nathan Gardner, Lyman Monroe, Daisuke Kihara, & Chiwook Park, Energetic coupling between ligand binding and dimerization in E. coli phosphoglycerate mutase, Biochemistry, 55: 1711-1723 (2016) PDF Abstract
112 2016 MF Lensink, S Velankar, A Kryshtafovych, S-Y Huang, D Schneidman-Duhovny, A Sali, J Segura, N Fernandez-Fuentes, S Viswanath, R Elber, S Grudinin, P Popov, E Neveu, H Lee, M Baek, S Park, L Heo, GR Lee, C Seok, S Qin, H-X Zhou, DW Ritchie, B Maigret, M-D Devignes, A Ghoorah, M Torchala, RAG Chaleil, PA. Bates, E Ben-Zeev, M Eisenstein, SS Negi, Z Weng, T Vreven, BG Pierce, TM Borrman, J Yu, F Ochsenbein, R Guerois, A Vangone, JPGLM Rodrigues, G van Zundert, M Nellen, L Xue, E Karaca, ASJ Melquiond, K Visscher, PL Kastritis, AMJJ Bonvin, X Xu, L Qiu, C Yan, J Li, Z Ma, J Cheng, X Zou, Y Shen, LX Peterson, H-R Kim, A Roy, X Han, J Esquivel-Rodriguez, D Kihara, X Yu, NJ Bruce, JC Fuller, RC Wade, I Anishchenko, PJ Kundrotas, IA Vakser, K Imai, K Yamada, T Oda, T Nakamura, K Tomii, C Pallara, M Romero-Durana, B Jimnez-Garca, IH Moal, J Frnandez-Recio, JY Joung, JY Kim, K Joo, J Lee, D Kozakov, S Vajda, S Mottarella, DR Hall, D Beglov, A Mamonov, B Xia, T Bohnuud, CA Del Carpio, E Ichiishi, N Marze, D Kuroda, SSR Burman, JJ Gray, E Chermak, L Cavallo, R Oliva, A Tovchigrechko, & SJ Wodak, Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1: 323-348 (2016) PDF Abstract
--- 2016 Daisuke Kihara, Computational protein function predictions, Methods, 93: 1-2 (2016) PDF Abstract
111 2016 Woong-Hee Shin, Mark G. Bures, & Daisuke Kihara, PatchSurfers: Two methods for local molecular property-based binding ligand prediction, Methods, 93: 41-50 (2016) PDF Abstract
110 2016 Xiaolei Zhu, Woong-Hee Shin, Hyungrae Kim, & Daisuke Kihara, Combined approach of Patch-Surfer and PL-PatchSurfer for protein-ligand binding prediction in CSAR 2013 and 2014, J. Chem. Info. Model., 56: 1088-1099 (2015) PDF Abstract
109 2016 Hyung-Rae Kim, & Daisuke Kihara, Protein structure prediction using residue- and fragment-environment potentials in CASP11, Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1: 105-117 (2016) PDF Abstract
108 2015 Ishita K Khan*, Qing Wei*, Samuel Chapman, Dukka BKC, & Daisuke Kihara (* equal contribution), The PFP and ESG protein function prediction methods in 2014: Effect of database updates and ensemble approaches, GigaScience, 4: 43 (2015) PDF Abstract
107 2015 Fabien Senechal, Melanie L'Enfant, Jean-Marc Domon, Emeline Rosiau, Marie-Jeanne Crepeau, Ogier Surcouf, Juan Esquivel-Rodriguez, Paulo Marcelo, Alain Mareck, Francois Guerineau, Hyung-Rae Kim, Jozef Mravec, Estelle Bonnin, Elisabeth Jamet, Daisuke Kihara, Patrice Lerouge, Marie-Christine Ralet, Jerome Pelloux, & Catherine Rayon, Tuning of pectine methylesterification: PECTIN METHYLESTERASE INHIBITOR 7 modulates the processive activity of co-expressed PME3 in a pH-dependent manner, J. Biol. Chem, 290: 23320-23335 (2015) PDF Abstract
106 2015 Woong-Hee Shin, Xiaolei Zhu, Mark Gregory Bures, & Daisuke Kihara, Three-dimensional compound comparison methods and their application in drug discovery, Molecules, 20: 12841-12862 (2015) PDF Abstract
105 2015 Juan Esquivel-Rodriguez, Yi Xiong, Xusi Han, Shuomeng Gang, Charles Christoffer, & Daisuke Kihara, Navigating 3D Electron Microscopy Maps with EM-SURFER, BMC Bioinformatics, 16: 181 (2015) PDF Abstract
104 2015 Abram Magner, Wojciech Szpankowski, & Daisuke Kihara, On the origin of protein superfamilies and superfolds, Scientific Reports, 5: 8166 (2015) PDF Abstract
103 2015 Yue Liu, Ju Sheng, Andrei Fokine, Geng, Meng, Woong-Hee Shin, Feng, Long, Richard J. Kuhn, Daisuke Kihara, & Michael G. Rossmann, Structure and inhibition of EV-D68, a virus that causes respiratory illness in children, Science 347: 71-74 (2015) PDF Abstract
102 2015 Xiaolei Zhu, Yi Xiong, & Daisuke Kihara, Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0, Bioinformatics, 31: 707-713 (2015) PDF Abstract
101 2015 Ishita K. Khan*, Qing Wei*, & Daisuke Kihara (* equal contribution), PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualizatoin tool, Bioinformatics, 31: 271-272 (2015) PDF Abstract
100 2015 Yuka Otsuka, Ai Muto, Rikiya Takeuchi, Chihiro Okada, Motokazu Ishikawa, Koichiro Nakamura, Natsuko Yamamoto, Hitomi Dose, Kenji Nakahigashi, Shigeki Tanishima, Sivasundaram Suharnan, Wataru Nomura, Toru Nakayashiki, Walid G. Aref, Barry R. Bocher, Tyrell Conway, Michael Gribskov, Daisuke Kihara, Kenneth E. Rudd, Yukako Tohsato, Barry L. Wanner, & Hirotada Mori, GenoBase: comprehensive resource database of Escherichia coli K-12, Nuc. Acid Research, 43: D606-D617 (2015) PDF Abstract
99 2014 Ishita K. Khan, Yuqian Chen, Tiange Dong, Xioawei Hong, Rikiya Takeuchi, Hirotada Mori, & Daisuke Kihara, Genome-scale identification and characterization of moonlighting proteins, Biology Direct., 9: 30 (2014) PDF Abstract
98 2014 Ishita K. Khan & Daisuke Kihara, Computational characterization of moonlighting proteins, Biochem. Soc. Trans. 42: 1780-1785 (2014) PDF Abstract
97 2014 Uma K Aryal, Yi Xiong, Zachary McBride, Daisuke Kihara, Jun Xie, Mark C Hall, & Daniel B Szymanski, A proteomic strategy for global analysis of plant protein complexes, The Plant cell, 26: 3867-82 (2014) PDF Abstract
96 2014 Bingjie Hu, Xiaolei Zhu, Lyman Monroe, Mark G. Bures, & Daisuke Kihara, PL-PatchSurfer: A novel molecular local surface-based method for exploring protein-ligand interactions, Int. J. Molecular Science, 15: 15122-15145 (2014) PDF Abstract
95 2014 Hyung-Rae Kim & Daisuke Kihara, Detecting local residue environment similarity for recognizing near-native structure models, Proteins: Structure, Function, and Bioinformatics, 82: 3255-3272 (2014) PDF Abstract
94 2014 Anna T. Olek, Catherine Rayon, Lee Makowski, Hyung Rae Kim, Peter Ciesielski, John Badger, Lake N. Paul, Subhangi Ghosh, Daisuke Kihara, Michael Crowley, Michael E. Himmel, Jeffrey T. Bolin, & Nicholas C. Carpita, The structure of the catalytic domain of a plant cellulose synthase and assembly into dimers, Plant Cell, 26: 2996-3009 (2014) PDF Abstract
93 2014 Atilla Sit & Daisuke Kihara, Comparison of Image Patches Using Local Moment Invariants, IEEE Transactions on Image Processing, 23: 2369-2379 (2014) PDF Abstract
92 2014 Lenna X Peterson, Xuejiao Kang, & Daisuke Kihara, Assessment of protein side-chain conformation prediction methods in different residue environments, Proteins: Structure, Function, and Bioinformatics, 82: 1971-1984 (2014) PDF Abstract
--- 2014 Jim Cavalcoli, Lonnie Welch, Bruce Aronow, Sorin Draghici, & Daisuke Kihara, The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio, Bioinformatics, 30: 148-149 (2014) PDF Abstract
91 2014 Sungho Won, Min-Seok Kwon, Manuel Mattheisen, Suyeon Park, Changsoon Park, Daisuke Kihara, Sven Cichon, Roel Ophoff, Markus M. Nothen, Marcella Rietschel, Max Baur, & Christoph Lange, Efficient strategy for detecting gene x gene joint action and its application in schizophrenia, Genetic Epidemiology, 38: 60-71 (2014) PDF Abstract
90 2014 Juan Esquivel-Rodriguez, Vianney Filos-Gonzalez, Bin Li, & Daisuke Kihara, Pairwise and multimeric protein-protein docking using the LZerD program suite, Methods in Molecular Biology, 1137: 209-234 (2014) PDF Abstract
89 2014 Yi Xiong, Juan Esquivel-Rodriguez, Lee Sael, & Daisuke Kihara, 3D-SURFER 2.0. Web platform for real-time search and characterization of protein surfaces, Methods in Molecular Biology, 1137: 105-117 (2014) PDF Abstract
88 2014 Yi Xiong, Dan Syzmanski, & Daisuke Kihara, Characterization and prediction of human protein-protein interactions, Biological Data Mining and Its Applications in Healthcare, X.-L. Li, S.-K. Ng, & J.T.L. Wang (eds), Chapter 9, pp.237-261, World Scientific, New Jersey, USA (2014) PDF Abstract
87 2013 Victor Padilla-Sanchez, Song Gao, Hyung Rae Kim, Daisuke Kihara, Lei Sun, Michael G Rossmann, & Venigalla B Rao, Structure-Function Analysis of the DNA Translocating Portal of the Bacteriophage T4 Packaging Machine, J. Mol. Biology, 426: 1019-1038 (2013) PDF Abstract
86 2013 Juan Esquivel-Rodriguez & Daisuke Kihara, Computational methods for constructing protein structure models from 3D electron microscopy maps, J. Structural Biology, 184: 93-102 (2013) PDF Abstract
85 2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Kilambi KP, Gray JJ, Popov P, Grudinin S, Esquivel-Rodriguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D., Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, Proteins, 81: 1980-1987 (2013) PDF Abstract
84 2013 Yi Xiong*, Xiaolei Zhu*, & Daisuke Kihara (* equal contribution), Ligand binding site identification, In silico Drug Discovery and Design Techniques. M. Lill (eds), Future Science, London, UK, Chapter 16, pp. 204-220 (2013) PDF Abstract
83 2013 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Toronen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Honigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Bjorne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bosnjak M, Panov P, Dzeroski S, Smuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I, A large-scale evaluation of computational protein function prediction, Nature Methods, 10: 221-227(2013) PDF Abstract
82 2013 Meghana Chitale*, Ishita K. Khan*, & Daisuke Kihara (* equal contribution), In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment, BMC Bioinformatics, 14 Suppl 3: S2 (2013) PDF Abstract
81 2013 David La, Misun Kong, William Hoffman, YounIm Choi & Daisuke Kihara, Predicting permanent and transient protein-protein interfaces, Proteins: Structure, Function, and Bioinformatics, 81: 805-818 (2013) PDF Abstract
80 2013 Mingjie Tang*, Kean Ming Tan*, Xin Lu Tan, Lee Sael, Meghana Chitale, Juan Esquivel-Rodriguez, & Daisuke Kihara (* equal contribution), Graphical models for protein function and structure predictions, Handbook of Biological Knowledge Discovery, Mourad Elloumi & Albert Y. Zomaya(eds.), Chapter 9, pp.191-222, Wiley (2013) PDF Abstract
79 2012 Chao Yuan, Hao Chen, & Daisuke Kihara, Effective inter-residue contact definitions for accurate protein fold recognition, BMC Bioinformatics, 13: 292 (2012) PDF Abstract
78 2012 Juan Esquivel-Rodriguez, & Daisuke Kihara, Effect of conformation sampling strategies in genetic algorithm for multiple protein docking, BMC Proceedings, 6 Suppl 7: S4 (2012) PDF Abstract
77 2012 Ishita Khan, Meghana Chitale, Catherine Rayon, & Daisuke Kihara, Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins, BMC Proceedings, 6 Suppl 7: S5 (2012) PDF Abstract
76 2012 Mario Abdel Messih, Meghana Chitale, Vladimir B. Bajic, Daisuke Kihara*, & Xin Gao* (* co-corresponding authors), Protein domain recurrence and order can enhance prediction of protein functions, Bioinformatics, 28: i440-i450 (2012) PDF Abstract
75 2012 Juan Esquivel-Rodriguez, Yifeng D. Yang, & Daisuke Kihara, Multi-LZerD: Multiple protein docking for asymmetric complexes, Proteins: Structure, Function, and Bioinformatics, 80: 1818-1833 (2012) PDF Abstract
74 2012 Juan Esquivel-Rodriguez & Daisuke Kihara, Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors, J Phys Chem B, 116: 6854-6861 (2012) PDF Abstract
73 2012 Elwood A. Mullins,Courtney M. Starks, Julie A. Francois, Lee Sael, Daisuke Kihara, & T. Joseph Kappock, Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability, Protein Science, 21: 686-696 (2012) PDF Abstract
72 2012 Michal Jamroz, Andrzej Kolinski, & Daisuke Kihara, Structural features that predict real-value fluctuations of globular proteins, Proteins: Structure, Function, and Bioinformatics, 80: 1425-1435 (2012) PDF Abstract
71 2012 Lee Sael*, Meghana Chitale*, & Daisuke Kihara (* equal contribution), Structure- and sequence-based function prediction for non-homologous proteins, Journal of Structural and Functional Genomics, 13: 111-123 (2012) PDF Abstract
70 2012 Bin Li & Daisuke Kihara, Protein Docking Prediction Using Predicted Protein-Protein Interface, BMC Bioinformatics, 13:7 (2012) PDF Abstract
69 2012 Lee Sael & Daisuke Kihara, Detecting Local Ligand-Binding Site Similarity in Non-Homologous Proteins by Surface Patch Comparison, Proteins: Str Funct. Bioinformatics, 80: 1177-1195 (2012) PDF Abstract
68 2012 Juan Esquivel-Rodríguez & Daisuke Kihara, Evaluation of multiple protein docking structures using correctly predicted pairwise subunits, BMC Bioinformatics, 13:S6 (2012) (Best paper award at GLBIO 2011, ISMB) PDF Abstract
67 2012 Lee Sael & Daisuke Kihara, Constructing patch-based ligand-binding pocket database for predicting function of proteins, BMC Bioinformatics, 13:S7 (2012) PDF Abstract
66 2012 David La & Daisuke Kihara, A novel method for protein-protein interaction site prediction using phylogenetic substitution models, Proteins: Structure, Function, and Bioinformatics, 80: 126-141 (2012) PDF Abstract
65 2011 Zhonglian Huang, Priyanka Surana, Daisuke Kihara, Richard Meilan, & Keith Woeste, JnCML-like, an EF-hand motif-containing gene seasonally upregulated in the transition zone of black walnut (Juglans nigra L.), American Journal of Molecular Biology, 1: 140-155 (2011) PDF Abstract
64 2011 Meghana Chitale, Shriphani Palakodety & Daisuke Kihara, Quantification of protein group coherence and pathway assignment using functional association, BMC Bioinformatics, 12:373 (2011) PDF Abstract
63 2011 SJ Fleishman, TA Whitehead, E-M Strauch, JE Corn, S Qin, H-X Zhou, JC Mitchell, ONA Demerdash, M Takeda-Shitaka, G Terashi, IH Moal, X Li, PA Bates, M Zacharias, H Park, J-S Ko, H Lee, C Seok, T Bourquard, J Bernauer, A Poupon, J Aze, S Soner, SK Ovali, P Ozbek, NB Tal, T Haliloglu, H Hwang, T Vreven, BG Pierce, Z Weng, L Perez-Cano, C Pons, J Fernandez-Recio, F Jiang, CH Robert, M Guharoy, S Liu, Y Huang, L Li, D Guo, Y Chen, Y Xiao, N London, Z Itzhaki, O Schueler-Furman, Y Inbar, V Patapov, M Cohen, G Schreiber, Y Tsuchiya, E Kanamori, DM Standley,H Nakamura, K Kinoshita, CM Driggers, RG Hall, JL Morgan, VL Hsu, J Zhan, Y Yang, Y Zhou, PL Kastritis, AMJJ Bonvin, W Zhang, CJ Camacho, KP Kilambi, B Weitzner, J Porter, A Sircar, JJ Gray, M Ohue, N Uchikoga, Y Matsuzaki, T Ishida, Y Akiyama, R Khashan, S Bush, D Fouches, A Tropsha, J Esquivel-Rodriguez, D Kihara, PB Stranges, R Jacak, B Kuhlman, SJ Wodak, J Janin, & D Baker, Community wide asssessment of protein-interface modeling using a protein design based benchmark, J. Mol. Biol, 414: 289-302 (2011) PDF Abstract
62 2011 Daisuke Kihara, Lee Sael, Rayan Chikhi, & Juan Esquivel-Rodriguez, Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking, Curr. Protein and Peptide Science, 12: 520-530 (2011) PDF Abstract
61 2011 Greta L Lundgaard, Natae E Daniels, Slovénie Pyndiah, Erica K Cassimere, Kazi M Ahmed, Amélie Rodrigue, Daisuke Kihara, Carol B Post, & Daitoku Sakamuro, Identification of a novel effector domain of BIN1 for cancer suppression, J. Cellular Biochemistry, 112: 2992-3001 (2011) PDF Abstract
60 2011 Balamurugan Jagadeesan, Amy E. Fleishman Littlejohn, Mary Anne Amalaradjou, Atul K. Singh, Krishna K. Mishra, David La, Daisuke Kihara, & Arun K. Bhunia, N-terminal Gly224-Gly411 Domain in Listeria Adhesion Protein Interacts with Host Receptor Hsp60, PLoS ONE, 6:e20694 (2011) PDF Abstract
59 2011 Pei-Fen Liu, Daisuke Kihara, & Chiwook Park, Energetics-based discovery of protein-ligand interactions on a proteomics scale, J. Mol. Biol., 408: 147-162 (2011) PDF Abstract
58 2011 Meghana Chitale & Daisuke Kihara, Computational protein function prediction: Framework and challenges, Protein function prediction for omics era, D. Kihara ed., Chapter 1, pp. 1-17, Springer. (2011) PDF Abstract
57 2011 Meghana Chitale & Daisuke Kihara, Enhanced sequence-based function prediction methods and application to functional similairty networks, Protein function prediction for omics era, D. Kihara ed., Chapter 2, pp. 19-34, Springer.(2011) PDF Abstract
56 2011 Rayan Chikhi, Lee Sael, & Daisuke Kihara, Protein binding ligand prediction using moment-based methods, Protein function prediction for omics era, D. Kihara ed., Chapter 8, pp. 145-163, Springer. (2011) PDF Abstract
55 2011 Hao Chen & Daisuke Kihara, Effect of using suboptimal alignments in template-based protein structure prediction, Proteins: Str. Funct. Bioinformatics, 79: 315-334 (2011) PDF Abstract
54 2010 Lee Sael & Daisuke Kihara, Binding ligand prediction for proteins using partial matching of local surface patches, International Journal of Molecular Sciences, 11:5009-5026 (2010) PDF Abstract
53 2010 Lee Sael & Daisuke Kihara, Protein surface representation for application to comparing low-resolution protein structure data, BMC Bioinformatics 11:S2. (2010) (Best Paper Award at GIW2010) PDF Abstract
--- 2010 Daisuke Kihara, Letter from Abroad: Research activity in Kihara Lab at Purdue University, Seibutsu Butsuri (Biophysics), (in Japanese) 50: 258-259 (2010) PDF
52 2010 Yifeng D Yang, Preston Spratt, Hao Chen, Changsoon Park & Daisuke Kihara, Sub-AQUA: Real-Value Quality Assessment of Protein Structure Models, PEDS Protein Engineering Design & Selection, 23: 617-632 (2010) PDF Abstract
51 2010 Troy Hawkins*, Meghana Chitale* & Daisuke Kihara (* equal contribution), Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP, BMC Bioinformatics, 11:265 (2010) PDF Abstract
50 2010 Rayan Chikhi, Lee Sael & Daisuke Kihara, Real-time ligand binding pocket database search using local surface descriptors, Proteins: Structure, Function, and Bioinformatics, 78:2007-2028.(2010) PDF Abstract
49 2010 Error estimation of template-based protein structure models., Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies, Andrzej Kolinski (ed.) , Springer-Verlag, Chapter 13, pp.295-314 (2010) PDF Abstract
48 2010 Lee Sael & Daisuke Kihara, Characterization and classification of local protein surfaces using self-organizing map, International Journal of Knowledge Discovery in Bioinformatics, 1, 32-47 (2010) PDF Abstract
47 2009 Vishwesh Venkatraman, Padmasini R Chakravarthy & Daisuke Kihara, Application of 3D Zernike descriptors to shape-based ligand similarity searching, J. Cheminformatics, 1:19 (2009) PDF Abstract
46 2009 Vishwesh Venkatraman, Yifeng D Yang, Lee Sael & Daisuke Kihara, Protein-protein docking using region-based 3D Zernike descriptors, BMC Bioinformatics, 10:407 (2009) PDF Abstract
45 2009 David La*, Juan Esquivel-Rodriguez*, Vishwesh Venkatraman, Bin Li, Lee Sael, Steven Ueng, Steven Ahrendt & Daisuke Kihara (* equal contribution), 3D-SURFER: software for high throughput surface comparison and analysis, Bioinformatics, 25: 2843-2844 (2009) PDF Abstract
44 2009 Vishwesh Venkatraman, Lee Sael & Daisuke Kihara, Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors, Cell Biochemistry and Biophysics 54: 23-32 (2009) PDF Abstract
43 2009 Meghana Chitale, Troy Hawkins, Changsoon Park, & Daisuke Kihara, ESG: Extended similarity group method for automated protein function prediction, Bioinformatics, 25: 1739-1745 (2009) PDF Abstract
42 2009 Lee Sael & Daisuke Kihara, Protein surface representation and comparison: New approaches in structural proteomics, Biological Data Mining, J Chen, S. Lonardi, (eds), Chapman & Hall/CRC Press, USA, Chapter 3, pp. 89-109 (2009) PDF Abstract
41 2009 Daisuke Kihara, Hao Chen & Yifeng Yang, Quality assessment of computational protein models, Current Protein and Peptide Science, 10: 216-228 (2009) PDF Abstract
40 2009 Troy Hawkins, Meghana Chitale, Stan Luban & Daisuke Kihara, PFP: Automated prediction of gene ontology functional annotations with confidence scores, Proteins: Structure, Function, and Bioinformatics, 74: 566-582 (2009) PDF Abstract
39 2008 Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Daisuke Kihara, Knight TF Jr, Pico AR, Siegele DA, Wanner BL, Welch RD, The emerging world of wikis, Science, 320: 1289-1290 (2008) PDF Abstract
38 2008 David La & Daisuke Kihara, Predicting binding interfaces of protein-protein interactions, (a book chapter in) Biological Data Mining in Protein Interaction Networks, X-L Li, S.K.Ng, (eds), Chapter 5, pp. 64-79, IGI-Global, Hershey, Philadelphia, USA (2008) Abstract
37 2008 Lee Sael, David La, Bin Li, Raif Rustamov & Daisuke Kihara, Rapid comparison of properties on protein surface, Proteins: Structure, Function, and Bioinformatics, 73: 1-10(2008) PDF Abstract
36 2008 Meghana Chitale, Troy Hawkins & Daisuke Kihara, Automated prediction of protein function from sequence, In Prediction of Protein Structure, Functions and Interactions, Janusz Bujnicki (ed), Chapter 3, pp. 64-86, John Wiley & Sons, Ltd. (2008) PDF Abstract
35 2008 Yifeng D. Yang, Changsoon Park & Daisuke Kihara, Threading without optimizing weighting factors for scoring function, Proteins: Structure, Function, and Bioinformatics, 73: 581-596 (2008) PDF Abstract
34 2008 Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov & Daisuke Kihara, Fast protein tertiary structure retrieval based on global surface shape similarity, Proteins: Structure, Function, and Bioinformatics, 72: 1259-1273 (2008) PDF Abstract
33 2008 Luo Si, Danni Yu, Daisuke Kihara & Yi Fang, Combining gene sequence similarity and textual information for gene function annotation in the literature, Information Retrieval, 11: 389-404 (2008) PDF
32 2008 Troy Hawkins, Meghana Chitale & Daisuke Kihara, New paradigm in protein function prediction for large scale omics analysis, Molecular BioSystems, 4: 223-231 (2008) PDF Abstract
31 2008 Hao Chen & Daisuke Kihara, Estimating quality of template-based protein models by alignment stability, Proteins: Struct. Funct. Bioinformatics, 71: 1255-1274 (2008) PDF Abstract
30 2008 Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani & Daisuke Kihara, Characterization of local geometry of protein surfaces with the visibility criterion, Proteins: Struct. Funct. Bioinformatics, 71: 670-683 (2008) PDF Abstract
29 2007 Mingwu Zhang, Daisuke Kihara & Sunil Prabhakar, Tracing lineage in multi-version scientific databases, IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE), 440-447 (2007) PDF
28 2007 Yu-Shen Liu, Min Liu, Daisuke Kihara & Karthik Ramani, Salient critical points for meshes, Proceedings of the 2007 ACM Solid and Physical Modeling, 277-282 (2007) PDF
27 2007 Stan Luban & Daisuke Kihara, Comparative genomics of small RNAs in bacterial genomes, Omics, 11: 58-73 (2007) PDF Abstract
26 2007 Troy Hawkins & Daisuke Kihara, Function prediction of uncharacterized proteins, J. Bioinformatics and Computational Biology, 5:1-30 (2007) PDF Abstract
25 2007 Daisuke Kihara, Troy Hawkins, Stan Luban Bin Li, Karthik Ramani, & Manish Agrawal, Protein function prediction in Proteomics Era, Proceedings of the International Symposium on Frontiers of Computational Science, Y Kaneda et al eds., pp. 143-148, Springer-Verlag, Berlin, Heidelberg. (2007) PDF
24 2006 Jianjun Hu, Yifeng David Yang & Daisuke Kihara, EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences, BMC Bioinformatics, 7:342 (2006) PDF Abstract
23 2006 Yen Hock Tan, He Huang & Daisuke Kihara, Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences, Proteins: Structure Funct, Bioinformatics, 64: 587-600 (2006) PDF Abstract
22 2006 Troy Hawkins, Stan Luban & Daisuke Kihara, Enhanced automated function prediction using distantly related sequences and contextual association by PFP, Protein Sci, 15:1550-1556 (2006) PDF Abstract
21 2006 Daisuke Kihara, Yifeng D. Yang & Troy Hawkins, Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools, Cancer Informatics, 2:25-35 (2006) PDF Abstract
20 2005 Jianjun Hu, Bin Li & Daisuke Kihara, Limitations and potentials of current motif discovery algorithms, Nucleic Acid Res. 33: 4899-4913 (2005) PDF Abstract
19 2005 Daisuke Kihara, The effect of long-range interactions on the secondary structure formation of proteins, Protein Science. 14: 1955-1963 (2005) PDF Abstract
18 2004 Daisuke Kihara, Biomolecular Structure Databases, Genome Function Research Handbook, Chapter 2. pp. 73-81. Yodosha Publishers, Tokyo, Japan (2004) Abstract
17 2004 Jeffrey Skolnick, Daisuke Kihara and Yang Zhang, Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm, Proteins: Structure, Funct. Bioinformatics 56:502-518 (2004) PDF Abstract
16 2004 Daisuke Kihara and Jeffrey Skolnick, Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q, Proteins: Structure, Funct. Bioinformatics 55: 464-473 (2004) PDF Abstract
15 2003 Daisuke Kihara and Jeffrey Skolnick, The PDB is a covering set of small protein structures, J. Mol. Biol. 334: 793-802 (2003) PDF Abstract
14 2003 Jeffrey Skolnick, Yang Zhang, Adrian Arakaki, Andrzej Kolinski, Michael Boniecki, Andras Szilagyi and Daisuke Kihara., TOUCHSTONE: a unified approach to protein structure prediction, Proteins: Structure, Funct. Genet. 53: Suppl.6: 469-479 (2003) PDF Abstract
13 2003 Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng J. Huang, Deyou Zheng, Gaetano T. Montelione, Andrzej Kolinski, and Jeffrey Skolnick, TOUCHSTONEX: Protein Structure Prediction Using Sparse NMR Data, Proteins: Structure, Funct. Genet. 53: 290-306 (2003) PDF Abstract
12 2002 Yang, Zhang, Daisuke Kihara and Jeffrey Skolnick, Local Energy Landscape Flattening: Parallel Hyperbolic Monte Carlo Sampling of Protein Folding, Proteins: Structure, Funct. Genet. 48: 192-201 (2002) PDF Abstract
11 2002 Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, Ab initio Protein Structure Prediction on a Genomic Scale: Application to the Mycoplasma genitalium Genome, Proc. Natl. Acad. Sci. USA, 99: 5993-5998 (2002) PDF Abstract
10 2001 Jeffrey Skolnick, Andrzej Kolinski, Daisuke Kihara, Marcos Betancourt, Piotr Rotkiewicz and Michael Boniecki, Ab initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering, and Structure Refinement, Proteins: Structure, Funct. Genet. 45 (Suppl 5): 149-156 (2001) PDF Abstract
9 2001 Daisuke Kihara, Genome Databases on the Internet, Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme) 46 (16 Suppl): 2639-2645 (2001) Abstract
8 2001 Daisuke Kihara and Minoru Kanehisa, Prediction of Membrane Proteins in Post-Genomic Era, Recent Res. Developments in Protein Engng. 1: 179-196 (2001) PDF
7 2001 Daisuke Kihara, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, TOUCHSTONE: An ab initio Protein Structure Prediction Method that Uses Threading-based Tertiary Restraints, Proc. Natl. Acad. Sci. USA 98: 10125-10130 (2001) PDF Abstract
6 2001 Andrzej Kolinski, Marcos Betancourt, Daisuke Kihara, Piotr Rotkiewicz and Jeffrey Skolnick, Generalized Comparative Modeling (GENCOMP): A Combination of Sequence Comparison, Threading, and Lattice Modeling for Protein Structure Prediction and Refinement, Proteins: Structure, Funct. Genet. 44: 133-149 (2001) PDF Abstract
5 2001 Jeffrey Skolnick and Daisuke Kihara, Defrosting the Frozen Approximation: PROSPECTOR - A New Approach to Threading, Proteins: Structure, Funct. Genet. 42: 319-331 (2001) PDF Abstract
4 2000 Daisuke Kihara and Minoru Kanehisa, Tandem Cluster of Membrane Proteins in Complete Genome Sequences, Genome Res. 10: 731-743 (2000) PDF Abstract
3 1998 Daisuke Kihara and Minoru Kanehisa, The Genome Projects and Bioinformatics, Iwanami Kouza (Iwanami Lecture Series): Gendai Igaku no Kiso (The Basis of Modern Medical Science), vol.1, Chap.11, pp: 215-235, Iwanami Shoten Publishers, Tokyo Japan (1998) Abstract
2 1998 Daisuke Kihara, Toshio Shimizu and Minoru Kanehisa, Prediction of Membrane Proteins Based on Classification of Transmembrane Segments, Protein Engng., 11: 961-970 (1998) PDF Abstract
1 1997 Daisuke Kihara, Minoru Kanehisa and Toshihisa Takagi, Internet Resources for Genome Research, Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme), 42(17 Suppl): 3090-3099 (1997) Abstract