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Paratope states in solution improve structure prediction and docking.
Fernández-Quintero ML, Vangone A, Loeffler JR, Seidler CA, Georges G, Liedl KR. Fernández-Quintero ML, et al. Among authors: vangone a. Structure. 2022 Mar 3;30(3):430-440.e3. doi: 10.1016/j.str.2021.11.001. Epub 2021 Nov 26. Structure. 2022. PMID: 34838187 Free 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: vangone a. 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.
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: vangone a. 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.
A random forest classifier for protein-protein docking models.
Barradas-Bautista D, Cao Z, Vangone A, Oliva R, Cavallo L. Barradas-Bautista D, et al. Among authors: vangone a. Bioinform Adv. 2021 Dec 10;2(1):vbab042. doi: 10.1093/bioadv/vbab042. eCollection 2022. Bioinform Adv. 2021. PMID: 36699405 Free PMC article.
Correction: Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody.
de Bruin RCG, Stam AGM, Vangone A, van Bergen En Henegouwen PMP, Verheul HMW, Sebestyén Z, Kuball J, Bonvin AMJJ, de Gruijl TD, van der Vliet HJ. de Bruin RCG, et al. Among authors: vangone a. J Immunol. 2017 May 1;198(9):3759. doi: 10.4049/jimmunol.1700317. J Immunol. 2017. PMID: 28416722 No abstract available.
32 results