Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures.

ABSTRACT: The ability to discriminate native structures from computer-generated misfolded ones is key to predicting the three-dimensional structure of a protein from its amino acid sequence. Here we describe an assessment of semiempirical methods for discriminating native protein structures from decoy models. The discrimination of decoys entails an analysis of a large number of protein structures, and provides a large-scale validation of quantum mechanical methods and their ability to accurately model proteins. We combine our analysis of semiempirical methods with a comparison of an AMBER force field to discriminate decoys in conjunction with a continuum solvent model. Protein decoys provide a rigorous and reliable benchmark for the evaluation of scoring functions, not only in their ability to accur

SUBMITTER: Wollacott AM 

PROVIDER: S-EPMC2523267 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature