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A dynamical view of binding affinity

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Contacts-based prediction of binding affinity in protein–protein complexes

Author(s): Anna Vangone, Alexandre MJJ Bonvin
Published in: eLife, Issue 4, 2015, ISSN 2050-084X
DOI: 10.7554/eLife.07454

Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes

Author(s): Cunliang Geng, Anna Vangone, Alexandre M.J.J. Bonvin
Published in: Protein Engineering Design and Selection, Issue 29/8, 2016, Page(s) 291-299, ISSN 1741-0126
DOI: 10.1093/protein/gzw020

PRODIGY: a web server for predicting the binding affinity of protein–protein complexes

Author(s): Li C. Xue, João Pglm Rodrigues, Panagiotis L. Kastritis, Alexandre Mjj Bonvin, Anna Vangone
Published in: Bioinformatics, 2016, Page(s) btw514, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btw514

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

Author(s): Thom Vreven, Iain H. Moal, Anna Vangone, Brian G. Pierce, Panagiotis L. Kastritis, Mieczyslaw Torchala, Raphael Chaleil, Brian Jiménez-García, Paul A. Bates, Juan Fernandez-Recio, Alexandre M.J.J. Bonvin, Zhiping Weng
Published in: Journal of Molecular Biology, Issue 427/19, 2015, Page(s) 3031-3041, ISSN 0022-2836
DOI: 10.1016/j.jmb.2015.07.016

Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody

Author(s): Renée C. G. de Bruin, Anita G. M. Stam, Anna Vangone, Paul M. P. van Bergen en Henegouwen, Henk M. W. Verheul, Zsolt Sebestyén, Jürgen Kuball, Alexandre M. J. J. Bonvin, Tanja D. de Gruijl, Hans J. van der Vliet
Published in: The Journal of Immunology, Issue 198/1, 2016, Page(s) 308-317, ISSN 0022-1767
DOI: 10.4049/jimmunol.1600948

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

Author(s): Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, J. P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, A. M. J. J. Bonvin
Published in: Journal of Computer-Aided Molecular Design, 2017, ISSN 0920-654X
DOI: 10.1007/s10822-017-0049-y

PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes

Author(s): Anna Vangone, Alexandre Bonvin
Published in: BIO-PROTOCOL, Issue 7/3, 2017, ISSN 2331-8325
DOI: 10.21769/BioProtoc.2124