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The ClusPro AbEMap web server for the prediction of antibody epitopes.
Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Beglov D, Vajda S, Kozakov D. Desta IT, et al. Among authors: kholodov y. Nat Protoc. 2023 Jun;18(6):1814-1840. doi: 10.1038/s41596-023-00826-7. Epub 2023 May 15. Nat Protoc. 2023. PMID: 37188806 Free PMC article. Review.
ClusPro LigTBM: Automated Template-based Small Molecule Docking.
Alekseenko A, Kotelnikov S, Ignatov M, Egbert M, Kholodov Y, Vajda S, Kozakov D. Alekseenko A, et al. Among authors: kholodov y. J Mol Biol. 2020 May 15;432(11):3404-3410. doi: 10.1016/j.jmb.2019.12.011. Epub 2019 Dec 19. J Mol Biol. 2020. PMID: 31863748 Free PMC article.
Mapping of antibody epitopes based on docking and homology modeling.
Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Sabitova M, Beglov D, Vajda S, Kozakov D. Desta IT, et al. Among authors: kholodov y. Proteins. 2023 Feb;91(2):171-182. doi: 10.1002/prot.26420. Epub 2022 Sep 30. Proteins. 2023. PMID: 36088633 Free PMC article.
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.
Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D, Kotelnikov S, Kazennov A, Grebenkin I, Kholodov Y, Kolosvari I, Perez A, Dill K, Kozakov D. Ignatov M, et al. Among authors: kholodov y. J Comput Aided Mol Des. 2019 Jan;33(1):119-127. doi: 10.1007/s10822-018-0176-0. Epub 2018 Nov 12. J Comput Aided Mol Des. 2019. PMID: 30421350 Free PMC article.
Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.
Padhorny D, Kazennov A, Zerbe BS, Porter KA, Xia B, Mottarella SE, Kholodov Y, Ritchie DW, Vajda S, Kozakov D. Padhorny D, et al. Among authors: kholodov y. Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):E4286-93. doi: 10.1073/pnas.1603929113. Epub 2016 Jul 13. Proc Natl Acad Sci U S A. 2016. PMID: 27412858 Free PMC article.