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Protein-protein interaction specificity is captured by contact preferences and interface composition.


ABSTRACT: Motivation:Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. Results:We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. Availability and implementation:CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. Contact:alessandra.carbone@lip6.fr. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Nadalin F 

PROVIDER: S-EPMC5860360 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Protein-protein interaction specificity is captured by contact preferences and interface composition.

Nadalin Francesca F   Carbone Alessandra A  

Bioinformatics (Oxford, England) 20180201 3


<h4>Motivation</h4>Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations.<h4>Results</h4>We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair pot  ...[more]

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