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

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10.1016/j.jmb.2015.07.016
 
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Vreven, Thom
Moal, Iain H.
Vangone, Anna
Pierce, Brian G.
Kastritis, Panagiotis L.
Torchala, Mieczyslaw
Chaleil, Raphael
Jiménez-García, Brian
Bates, Paul A.
Fernández-Recio, Juan
Bonvin, Alexandre M. J. J.
Weng, Zhiping
Document typeArticle
Defense date2015-09-25
PublisherElsevier
Rights accessOpen Access
All rights reserved. This work is protected by the corresponding intellectual and industrial property rights. Without prejudice to any existing legal exemptions, reproduction, distribution, public communication or transformation of this work are prohibited without permission of the copyright holder
ProjectDESARROLLO DE NUEVAS METODOLOGIAS DE DOCKING ENTRE PROTEINAS PARA LOS RETOS DE INTERACTOMICA Y MEDICINA PERSONALIZADA (MINECO-BIO2013-48213-R)
Abstract
We present an updated and integrated version of our widely used protein–protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein–protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody–antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top 10 docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r = 0.52 overall and r = 0.72 for the rigid complexes.
CitationVreven, Thom [et al.]. Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. "Journal of Molecular Biology", 25 Setembre 2015, vol. 427, núm. 19, p. 3031-3041. 
URIhttp://hdl.handle.net/2117/86753
DOI10.1016/j.jmb.2015.07.016
ISSN0022-2836
Publisher versionhttp://www.sciencedirect.com/science/article/pii/S0022283615004180
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