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Update of the ATTRACT force field for the prediction of protein–protein binding affinity
Author(s) -
Chéron JeanBaptiste,
Zacharias Martin,
Antonczak Serge,
Fiorucci Sébastien
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24836
Subject(s) - affinities , binding affinities , force field (fiction) , docking (animal) , computational biology , chemistry , macromolecule , plasma protein binding , computational chemistry , computer science , biology , stereochemistry , biochemistry , artificial intelligence , receptor , medicine , nursing
Determining the protein–protein interactions is still a major challenge for molecular biology. Docking protocols has come of age in predicting the structure of macromolecular complexes. However, they still lack accuracy to estimate the binding affinities, the thermodynamic quantity that drives the formation of a complex. Here, an updated version of the protein–protein ATTRACT force field aiming at predicting experimental binding affinities is reported. It has been designed on a dataset of 218 protein–protein complexes. The correlation between the experimental and predicted affinities reaches 0.6, outperforming most of the available protocols. Focusing on a subset of rigid and flexible complexes, the performance raises to 0.76 and 0.69, respectively. © 2017 Wiley Periodicals, Inc.