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Page 1
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton … See abstract for full author list ➔ Zhou N, et al. Among authors: antczak m. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine.
Hernandez G, Osinski A, Majumdar A, Eitson JL, Antczak M, Pawłowski K, Niederstrasser H, Servage KA, Posner B, Schoggins JW, Ready JA, Tagliabracci VS. Hernandez G, et al. Among authors: antczak m. bioRxiv [Preprint]. 2024 Nov 25:2024.11.22.624893. doi: 10.1101/2024.11.22.624893. bioRxiv. 2024. PMID: 39651217 Free PMC article. Preprint.
RNA-Puzzles Round V: blind predictions of 23 RNA structures.
Bu F, Adam Y, Adamiak RW, Antczak M, de Aquino BRH, Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ, Bujnicki JM, Carpenter KA, Chacon J, Chen SJ, Chiu W, Cordero P, Das NK, Das R, Dawson WK, DiMaio F, Ding F, Dock-Bregeon AC, Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferré-D'Amaré AR, Geniesse C, Ghanim GE, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC, Kurciński M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN, Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Trachman RJ 3rd, Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J, Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T, Zhang D, Zhang S, Żyła A, Westhof E, Miao Z. Bu F, et al. Among authors: antczak m. Nat Methods. 2024 Dec 2. doi: 10.1038/s41592-024-02543-9. Online ahead of print. Nat Methods. 2024. PMID: 39623050 Free article.
Knotted artifacts in predicted 3D RNA structures.
Gren BA, Antczak M, Zok T, Sulkowska JI, Szachniuk M. Gren BA, et al. Among authors: antczak m. PLoS Comput Biol. 2024 Jun 20;20(6):e1011959. doi: 10.1371/journal.pcbi.1011959. eCollection 2024 Jun. PLoS Comput Biol. 2024. PMID: 38900780 Free PMC article.
RNAhugs web server for customized 3D RNA structure alignment.
Zurkowski M, Swiercz M, Wozny F, Antczak M, Szachniuk M. Zurkowski M, et al. Among authors: antczak m. Nucleic Acids Res. 2024 Jul 5;52(W1):W348-W353. doi: 10.1093/nar/gkae259. Nucleic Acids Res. 2024. PMID: 38587206 Free PMC article.
80 results