Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.

ABSTRACT: Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the interaction signal and the contribution of docking information compared to evolutionary information showing that the combination of the two improves partner identification. On the other hand, since protein interactions usually occur in crowded environments with several competing partners, we realized a thorough analysis of the interactions of proteins with true partners but also with non-partners to ev

SUBMITTER: Lopes A 

PROVIDER: S-EPMC3854762 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature