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Page 1
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: desta i. Proteins. 2021 Dec;89(12):1800-1823. doi: 10.1002/prot.26222. Epub 2021 Sep 13. Proteins. 2021. PMID: 34453465 Free PMC article.
What method to use for protein-protein docking?
Porter KA, Desta I, Kozakov D, Vajda S. Porter KA, et al. Among authors: desta i. Curr Opin Struct Biol. 2019 Apr;55:1-7. doi: 10.1016/j.sbi.2018.12.010. Epub 2019 Feb 1. Curr Opin Struct Biol. 2019. PMID: 30711743 Free PMC article. Review.
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Hon… See abstract for full author list ➔ Lensink MF, et al. Among authors: desta i. Proteins. 2019 Dec;87(12):1200-1221. doi: 10.1002/prot.25838. Epub 2019 Oct 25. Proteins. 2019. PMID: 31612567 Free PMC article.
Improved cluster ranking in protein-protein docking using a regression approach.
Sotudian S, Desta IT, Hashemi N, Zarbafian S, Kozakov D, Vakili P, Vajda S, Paschalidis IC. Sotudian S, et al. Among authors: desta it. Comput Struct Biotechnol J. 2021 Apr 20;19:2269-2278. doi: 10.1016/j.csbj.2021.04.028. eCollection 2021. Comput Struct Biotechnol J. 2021. PMID: 33995918 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: desta i. Proteins. 2021 Dec;89(12):1922-1939. doi: 10.1002/prot.26209. Epub 2021 Aug 19. Proteins. 2021. PMID: 34368994 Free PMC article.
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. Proteins. 2023 Feb;91(2):171-182. doi: 10.1002/prot.26420. Epub 2022 Sep 30. Proteins. 2023. PMID: 36088633 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.
18 results