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Year Number of Results
2018 1
2019 4
2020 3
2021 3
2022 7
2023 8
2024 1

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22 results

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Page 1
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.
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.
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.
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.
Paul I, Bolzan D, Youssef A, Gagnon KA, Hook H, Karemore G, Oliphant MUJ, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen CS, Hu P, Denis GV, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy SK, Emili A. Paul I, et al. Among authors: kotelnikov s. Nat Commun. 2023 Feb 8;14(1):688. doi: 10.1038/s41467-023-36122-x. Nat Commun. 2023. PMID: 36755019 Free PMC article.
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Vela… See abstract for full author list ➔ Lensink MF, et al. Among authors: kotelnikov s. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 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.
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.
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.
22 results