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Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server.
Kotelnikov S, Ashizawa R, Popov KI, Khan O, Ignatov M, Li SX, Hassan M, Coutsias EA, Poda G, Padhorny D, Tropsha A, Vajda S, Kozakov D. Kotelnikov S, et al. Proteins. 2023 Dec;91(12):1822-1828. doi: 10.1002/prot.26587. Epub 2023 Sep 11. Proteins. 2023. PMID: 37697630
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: kotelnikov s. 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.
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: kotelnikov s. 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.
Conservation of binding properties in protein models.
Egbert M, Porter KA, Ghani U, Kotelnikov S, Nguyen T, Ashizawa R, Kozakov D, Vajda S. Egbert M, et al. Among authors: kotelnikov s. Comput Struct Biotechnol J. 2021 Apr 25;19:2549-2566. doi: 10.1016/j.csbj.2021.04.048. eCollection 2021. Comput Struct Biotechnol J. 2021. PMID: 34025942 Free PMC article.
Assessing the binding properties of CASP14 targets and models.
Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Egbert M, et al. Among authors: kotelnikov s. Proteins. 2021 Dec;89(12):1922-1939. doi: 10.1002/prot.26209. Epub 2021 Aug 19. Proteins. 2021. PMID: 34368994 Free PMC article.
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Giełdoń A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, Zięba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Xu X, Zhang S, Zou X,… See abstract for full author list ➔ Lensink MF, et al. Among authors: kotelnikov s. Proteins. 2021 Dec;89(12):1800-1823. doi: 10.1002/prot.26222. Epub 2021 Sep 13. Proteins. 2021. PMID: 34453465 Free PMC article.
Side-chain Packing Using SE(3)-Transformer.
Jindal A, Kotelnikov S, Padhorny D, Kozakov D, Zhu Y, Chowdhury R, Vajda S. Jindal A, et al. Among authors: kotelnikov s. Pac Symp Biocomput. 2022;27:46-55. Pac Symp Biocomput. 2022. PMID: 34890135 Free PMC article.
50 results