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Year Number of Results
1987 1
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1990 1
1996 2
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2000 1
2001 2
2002 1
2003 1
2005 2
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2008 2
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2017 3
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2019 6
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53 results

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Page 1
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.
Ligand interaction landscape of transcription factors and essential enzymes in E. coli.
Peng H, Kotelnikov S, Egbert ME, Ofaim S, Stevens GC, Phanse S, Saccon T, Ignatov M, Dutta S, Istace Z, Moutaoufik MT, Aoki H, Kewalramani N, Sun J, Gong Y, Padhorny D, Poda G, Alekseenko A, Porter KA, Jones G, Rodionova I, Guo H, Pogoutse O, Datta S, Saier M, Crovella M, Vajda S, Moreno-Hagelsieb G, Parkinson J, Segre D, Babu M, Kozakov D, Emili A. Peng H, et al. Among authors: kotelnikov s. Cell. 2025 Mar 6;188(5):1441-1455.e15. doi: 10.1016/j.cell.2025.01.003. Epub 2025 Jan 24. Cell. 2025. PMID: 39862855 Free article.
High Accuracy Prediction of PROTAC Complex Structures.
Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. Ignatov M, et al. Among authors: kotelnikov s. J Am Chem Soc. 2023 Apr 5;145(13):7123-7135. doi: 10.1021/jacs.2c09387. Epub 2023 Mar 24. J Am Chem Soc. 2023. PMID: 36961978 Free PMC article.
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: kotelnikov s. 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.
Light-mediated multi-target protein degradation using arylazopyrazole photoswitchable PROTACs (AP-PROTACs).
Zhang Q, Kounde CS, Mondal M, Greenfield JL, Baker JR, Kotelnikov S, Ignatov M, Tinworth CP, Zhang L, Conole D, De Vita E, Kozakov D, McCluskey A, Harling JD, Fuchter MJ, Tate EW. Zhang Q, et al. Among authors: kotelnikov s. Chem Commun (Camb). 2022 Sep 29;58(78):10933-10936. doi: 10.1039/d2cc03092f. Chem Commun (Camb). 2022. PMID: 36065962 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.
Opinion: Protein folds vs. protein folding: Differing questions, different challenges.
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Chen SJ, et al. Among authors: kotelnikov s. Proc Natl Acad Sci U S A. 2023 Jan 3;120(1):e2214423119. doi: 10.1073/pnas.2214423119. Epub 2022 Dec 29. Proc Natl Acad Sci U S A. 2023. PMID: 36580595 Free PMC article. No abstract available.
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: kotelnikov s. Proteins. 2023 Feb;91(2):171-182. doi: 10.1002/prot.26420. Epub 2022 Sep 30. Proteins. 2023. PMID: 36088633 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.
53 results