| The ClusPro web server for protein–protein docking D Kozakov, DR Hall, B Xia, KA Porter, D Padhorny, C Yueh, D Beglov, ... Nature protocols 12 (2), 255-278, 2017 | 2834 | 2017 |
| Allostery in its many disguises: from theory to applications SJ Wodak, E Paci, NV Dokholyan, IN Berezovsky, A Horovitz, J Li, ... Structure 27 (4), 566-578, 2019 | 341 | 2019 |
| 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 |
| Actionable cytopathogenic host responses of human alveolar type 2 cells to SARS-CoV-2 RM Hekman, AJ Hume, RK Goel, KM Abo, J Huang, BC Blum, RB Werder, ... Molecular cell 81 (1), 212, 2021 | 126 | 2021 |
| 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 | 103 | 2021 |
| Protein folds vs. protein folding: Differing questions, different challenges SJ Chen, M Hassan, RL Jernigan, K Jia, D Kihara, A Kloczkowski, ... Proceedings of the National Academy of Sciences 120 (1), e2214423119, 2023 | 88 | 2023 |
| Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds D Padhorny, A Kazennov, BS Zerbe, KA Porter, B Xia, SE Mottarella, ... Proceedings of the National Academy of Sciences 113 (30), E4286-E4293, 2016 | 78 | 2016 |
| Improved docking of protein models by a combination of alphafold2 and cluspro U Ghani, I Desta, A Jindal, O Khan, G Jones, N Hashemi, S Kotelnikov, ... BioRxiv, 2021.09. 07.459290, 2021 | 71 | 2021 |
| Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery PC Havugimana, RK Goel, S Phanse, A Youssef, D Padhorny, ... Nature communications 13 (1), 4043, 2022 | 56 | 2022 |
| ClusPro-DC: Dimer classification by the CLUSPRO server for protein–protein docking C Yueh, DR Hall, B Xia, D Padhorny, D Kozakov, S Vajda Journal of molecular biology 429 (3), 372-381, 2017 | 50 | 2017 |
| 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 | 45 | 2023 |
| Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking KA Porter, D Padhorny, I Desta, M Ignatov, D Beglov, S Kotelnikov, Z Sun, ... Proteins: Structure, Function, and Bioinformatics 87 (12), 1241-1248, 2019 | 23 | 2019 |
| Protein–ligand docking using FFT based sampling: D3R case study D Padhorny, DR Hall, H Mirzaei, AB Mamonov, M Moghadasi, ... Journal of computer-aided molecular design 32, 225-230, 2018 | 22 | 2018 |
| Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4 S Kotelnikov, A Alekseenko, C Liu, M Ignatov, D Padhorny, E Brini, ... Journal of computer-aided molecular design 34, 179-189, 2020 | 18 | 2020 |
| Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge M Ignatov, C Liu, A Alekseenko, Z Sun, D Padhorny, S Kotelnikov, ... Journal of computer-aided molecular design 33, 119-127, 2019 | 17 | 2019 |
| Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45 A Khramushin, O Marcu, N Alam, O Shimony, D Padhorny, E Brini, KA Dill, ... Proteins: Structure, Function, and Bioinformatics 88 (8), 1037-1049, 2020 | 15 | 2020 |
| Assessing the binding properties of CASP14 targets and models M Egbert, U Ghani, R Ashizawa, S Kotelnikov, T Nguyen, I Desta, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1922-1939, 2021 | 14 | 2021 |
| ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking D Padhorny, KA Porter, M Ignatov, A Alekseenko, D Beglov, S Kotelnikov, ... Proteins: Structure, Function, and Bioinformatics 88 (8), 1082-1090, 2020 | 14 | 2020 |
| Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT I Paul, D Bolzan, A Youssef, KA Gagnon, H Hook, G Karemore, ... Nature communications 14 (1), 688, 2023 | 13 | 2023 |
| Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap G Jones, A Jindal, U Ghani, S Kotelnikov, M Egbert, N Hashemi, S Vajda, ... Biological Crystallography 78 (6), 690-697, 2022 | 9 | 2022 |
Dima KozakovProfessor, Department of Applied Mathematics and StatisticsПідтверджена електронна адреса в stonybrook.edu
