A generalized knowledge-based discriminatory function for biomolecular interactions.

ABSTRACT: Several novel and established knowledge-based discriminatory function formulations and reference state derivations have been evaluated to identify parameter sets capable of distinguishing native and near-native biomolecular interactions from incorrect ones. We developed the r.m.r function, a novel atomic level radial distribution function with mean reference state that averages over all pairwise atom types from a reduced atom type composition, using experimentally determined intermolecular complexes in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB) as the information sources. We demonstrate that r.m.r had the best discriminatory accuracy and power for protein-small molecule and protein-DNA interactions, regardless of whether the native complex was included or exclu

SUBMITTER: Bernard B 

PROVIDER: S-EPMC2891153 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature