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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 accurately identify native structures but also to be computationally tractable to sample a large set of non-native models.

SUBMITTER: Wollacott AM

PROVIDER: S-EPMC2523267 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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

Wollacott Andrew M AM Merz Kenneth M KM

Journal of chemical theory and computation 20070101 4

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 pro ...[more]

PMID: 18728758

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