Integrating atom-based and residue-based scoring functions for protein-protein docking.

ABSTRACT: Most scoring functions for protein-protein docking algorithms are either atom-based or residue-based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom-based terms. Here we combine ZRANK's atom-based potentials with five residue-based potentials published by other labs, as well as an atom-based potential IFACE that we published after ZRANK. We simultaneously optimized the weights for selected combinations of terms in the scoring function, using decoys generated with the protein-protein docking algorithm ZDOCK. We performed rigorous cross validation of the combinations using 96 test cases

SUBMITTER: Vreven T 

PROVIDER: S-EPMC3190152 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature