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Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Vreven T, et al. Among authors: torchala m. J Mol Biol. 2015 Sep 25;427(19):3031-41. doi: 10.1016/j.jmb.2015.07.016. Epub 2015 Jul 29. J Mol Biol. 2015. PMID: 26231283 Free PMC article.
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Lensink MF, et al. Among authors: torchala m. Proteins. 2016 Sep;84 Suppl 1(Suppl Suppl 1):323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1. Proteins. 2016. PMID: 27122118 Free PMC article.
A Guide for Protein-Protein Docking Using SwarmDock.
Moal IH, Chaleil RAG, Torchala M, Bates PA. Moal IH, et al. Among authors: torchala m. Methods Mol Biol. 2020;2165:199-216. doi: 10.1007/978-1-0716-0708-4_11. Methods Mol Biol. 2020. PMID: 32621226
SwarmDock: a server for flexible protein-protein docking.
Torchala M, Moal IH, Chaleil RA, Fernandez-Recio J, Bates PA. Torchala M, et al. Bioinformatics. 2013 Mar 15;29(6):807-9. doi: 10.1093/bioinformatics/btt038. Epub 2013 Jan 23. Bioinformatics. 2013. PMID: 23343604
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