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2022 6
2023 11
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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. 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. Pac Symp Biocomput. 2022;27:46-55. Pac Symp Biocomput. 2022. PMID: 34890135 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, Velankar S,… See abstract for full author list ➔ Lensink MF, et al. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
Mapping the binding sites of challenging drug targets.
Wakefield AE, Kozakov D, Vajda S. Wakefield AE, et al. Curr Opin Struct Biol. 2022 Aug;75:102396. doi: 10.1016/j.sbi.2022.102396. Epub 2022 May 27. Curr Opin Struct Biol. 2022. PMID: 35636004 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. Nat Commun. 2023 Feb 8;14(1):688. doi: 10.1038/s41467-023-36122-x. Nat Commun. 2023. PMID: 36755019 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. 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.
17 results