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| 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 | 58 | 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 | 50 | 2023 |
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| ClusPro LigTBM: Automated template-based small molecule docking A Alekseenko, S Kotelnikov, M Ignatov, M Egbert, Y Kholodov, S Vajda, ... Journal of molecular biology 432 (11), 3404-3410, 2020 | 22 | 2020 |
| 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 | 19 | 2019 |
| AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence A Davila, Z Xu, S Li, J Rozewicki, J Wilamowski, S Kotelnikov, D Kozakov, ... Bioinformatics Advances 2 (1), vbac015, 2022 | 18 | 2022 |
| 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 |
| 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 | 16 | 2023 |
| Light-mediated multi-target protein degradation using arylazopyrazole photoswitchable PROTACs (AP-PROTACs) Q Zhang, CS Kounde, M Mondal, JL Greenfield, JR Baker, S Kotelnikov, ... Chemical Communications (Cambridge, England) 58 (78), 10933, 2022 | 15 | 2022 |
| 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 | 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 | 13 | 2021 |
| 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 | 10* | 2023 |
| High Accuracy Prediction of PROTAC Complex Structures M Ignatov, A Jindal, S Kotelnikov, D Beglov, G Posternak, X Tang, ... Journal of the American Chemical Society 145 (13), 7123-7135, 2023 | 9 | 2023 |
| 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 | 9 | 2020 |
| Mapping of antibody epitopes based on docking and homology modeling IT Desta, S Kotelnikov, G Jones, U Ghani, M Abyzov, Y Kholodov, ... Proteins: Structure, Function, and Bioinformatics 91 (2), 171-182, 2023 | 6 | 2023 |
| Side-chain packing using se (3)-transformer A Jindal, S Kotelnikov, D Padhorny, D Kozakov, Y Zhu, R Chowdhury, ... PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022, 46-55, 2021 | 5 | 2021 |
| 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, ... Acta Crystallographica Section D: Structural Biology 78 (6), 690-697, 2022 | 4 | 2022 |
| Conservation of binding properties in protein models M Egbert, KA Porter, U Ghani, S Kotelnikov, T Nguyen, R Ashizawa, ... Computational and structural biotechnology journal 19, 2549-2566, 2021 | 4 | 2021 |
