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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: bonvin am. 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.
Refinement of protein structures in explicit solvent.
Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M. Linge JP, et al. Among authors: bonvin am. Proteins. 2003 Feb 15;50(3):496-506. doi: 10.1002/prot.10299. Proteins. 2003. PMID: 12557191
Data-driven docking: HADDOCK's adventures in CAPRI.
van Dijk AD, de Vries SJ, Dominguez C, Chen H, Zhou HX, Bonvin AM. van Dijk AD, et al. Among authors: bonvin am. Proteins. 2005 Aug 1;60(2):232-8. doi: 10.1002/prot.20563. Proteins. 2005. PMID: 15981252
Flexible protein-protein docking.
Bonvin AM. Bonvin AM. Curr Opin Struct Biol. 2006 Apr;16(2):194-200. doi: 10.1016/j.sbi.2006.02.002. Epub 2006 Feb 17. Curr Opin Struct Biol. 2006. PMID: 16488145 Review.
268 results