Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.

ABSTRACT: The paper presents analysis of our template-based and free docking predictions in the joint CASP12/CAPRI37 round. A new scoring function for template-based docking was developed, benchmarked on the Dockground resource, and applied to the targets. The results showed that the function successfully discriminates the incorrect docking predictions. In correctly predicted targets, the scoring function was complemented by other considerations, such as consistency of the oligomeric states among templates, similarity of the biological functions, biological interface relevance, etc. The scoring function still does not distinguish well biological from crystal packing interfaces, and needs further development for the docking of bundles of α-helices. In the case of the trimeric targets, sequence-based

SUBMITTER: Kundrotas PJ 

PROVIDER: S-EPMC5820180 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature