| Community-wide assessment of protein-interface modeling suggests improvements to design methodology SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ... Journal of molecular biology 414 (2), 289-302, 2011 | 159 | 2011 |
| Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, ... Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 | 128 | 2019 |
| De novo main-chain modeling for EM maps using MAINMAST G Terashi, D Kihara Nature communications 9 (1), 1618, 2018 | 125 | 2018 |
| Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ... Proteins: Structure, Function, and Bioinformatics 81 (11), 1980-1987, 2013 | 115 | 2013 |
| Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment MF Lensink, G Brysbaert, T Mauri, N Nadzirin, S Velankar, RAG Chaleil, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021 | 104 | 2021 |
| Protein docking model evaluation by 3D deep convolutional neural networks X Wang, G Terashi, CW Christoffer, M Zhu, D Kihara Bioinformatics 36 (7), 2113-2118, 2020 | 102 | 2020 |
| Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning SR Maddhuri Venkata Subramaniya, G Terashi, D Kihara Nature methods 16 (9), 911-917, 2019 | 99 | 2019 |
| Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge CL Lawson, A Kryshtafovych, PD Adams, PV Afonine, ML Baker, ... Nature methods 18 (2), 156-164, 2021 | 91 | 2021 |
| SHREC 2020: Classification in cryo-electron tomograms I Gubins, ML Chaillet, G van Der Schot, RC Veltkamp, F Förster, Y Hao, ... Computers & Graphics 91, 279-289, 2020 | 68 | 2020 |
| Modeling disordered protein interactions from biophysical principles LX Peterson, A Roy, C Christoffer, G Terashi, D Kihara PLoS computational biology 13 (4), e1005485, 2017 | 63 | 2017 |
| Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning X Wang, E Alnabati, TW Aderinwale, SRMV Subramaniya, G Terashi, ... Biophysical Journal 120 (3), 81a, 2021 | 54 | 2021 |
| Real-time structure search and structure classification for AlphaFold protein models T Aderinwale, V Bharadwaj, C Christoffer, G Terashi, Z Zhang, ... Communications biology 5 (1), 316, 2022 | 51 | 2022 |
| Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment MF Lensink, G Brysbaert, N Raouraoua, PA Bates, M Giulini, RV Honorato, ... Proteins: Structure, Function, and Bioinformatics 91 (12), 1658-1683, 2023 | 43 | 2023 |
| CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps M Shekhar, G Terashi, C Gupta, D Sarkar, G Debussche, NJ Sisco, ... Matter 4 (10), 3195-3216, 2021 | 40 | 2021 |
| Modeling the assembly order of multimeric heteroprotein complexes LX Peterson, Y Togawa, J Esquivel-Rodriguez, G Terashi, C Christoffer, ... PLoS computational biology 14 (1), e1005937, 2018 | 40 | 2018 |
| Residue-wise local quality estimation for protein models from cryo-EM maps G Terashi, X Wang, SR Maddhuri Venkata Subramaniya, JJG Tesmer, ... Nature methods 19 (9), 1116-1125, 2022 | 35 | 2022 |
| The SKE‐DOCK server and human teams based on a combined method of shape complementarity and free energy estimation G Terashi, M Takeda‐Shitaka, K Kanou, M Iwadate, D Takaya, ... Proteins: Structure, Function, and Bioinformatics 69 (4), 866-872, 2007 | 35 | 2007 |
| Bioinformatics based Ligand-Docking and in-silico screening D Takaya, M Takeda-Shitaka, G Terashi, K Kanou, M Iwadate, ... Chemical and Pharmaceutical Bulletin 56 (5), 742-744, 2008 | 33 | 2008 |
| Fams‐ace: A combined method to select the best model after remodeling all server models G Terashi, M Takeda‐Shitaka, K Kanou, M Iwadate, D Takaya, A Hosoi, ... Proteins: Structure, Function, and Bioinformatics 69 (S8), 98-107, 2007 | 32 | 2007 |
| CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning X Wang, G Terashi, D Kihara Nature Methods 20 (11), 1739-1747, 2023 | 30 | 2023 |
Daisuke KiharaProfessor of Biological Sciences and Computer Science, Showalter University Faculty Scholar, PurdueVerified email at purdue.edu
