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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: 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.
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. Xue LC, et al. Among authors: vangone a. Bioinformatics. 2016 Dec 1;32(23):3676-3678. doi: 10.1093/bioinformatics/btw514. Epub 2016 Aug 8. Bioinformatics. 2016. PMID: 27503228
An important aspect of this is the ability to accurately predict the binding strength for a given protein-protein complex. Here we present PROtein binDIng enerGY prediction (PRODIGY), a web server to predict the binding affinity of protein-protein complexes from the …
An important aspect of this is the ability to accurately predict the binding strength for a given protein-protein complex. Here we pr …
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ. Kurkcuoglu Z, et al. Among authors: vangone a. J Comput Aided Mol Des. 2018 Jan;32(1):175-185. doi: 10.1007/s10822-017-0049-y. Epub 2017 Aug 22. J Comput Aided Mol Des. 2018. PMID: 28831657 Free PMC article.
PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes.
Vangone A, Bonvin AMJJ. Vangone A, et al. Bio Protoc. 2017 Feb 5;7(3):e2124. doi: 10.21769/BioProtoc.2124. eCollection 2017 Feb 5. Bio Protoc. 2017. PMID: 34458447 Free PMC article.
Many efforts have been devoted to unraveling principles of protein-protein interactions. Recently, we introduced a simple but robust descriptor of binding affinity based only on structural properties of a protein-protein complex. In Vangone and Bonvin (2015), …
Many efforts have been devoted to unraveling principles of protein-protein interactions. Recently, we introduced a simple but robust …
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.
32 results