HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors.

ABSTRACT: The HADDOCK score, a scoring function for both protein-protein and protein-nucleic acid modeling, has been successful in selecting near-native docking poses in a variety of cases, including those of the CAPRI blind prediction experiment. However, it has yet to be optimized for small molecules, and in particular inhibitors of protein-protein interactions, that constitute an "unmined gold reserve" for drug design ventures. We describe here HADDOCK(2P2I), a biophysical model capable of predicting the binding affinity of protein-protein complex inhibitors close to experimental error (~2-fold larger). The algorithm was trained and 4-fold cross-validated against experimental data for 27 inhibitors targeting 7 protein-protein complexes of various functions and tested on an independent set of 24 d

SUBMITTER: Kastritis PL 

PROVIDER: S-EPMC3966529 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature