Transferable coarse grain nonbonded interaction model for amino acids

Russell Devane, Wataru Shinoda, Preston B. Moore, Michael L. Klein

Research output: Contribution to journalArticlepeer-review

104 Citations (Scopus)

Abstract

The large quantity of protein sequences being generated from genomic data has greatly outpaced the throughput of experimental protein structure determining methods and consequently brought urgency to the need for accurate protein structure prediction tools. Reduced resolution, or coarse grained (CG) models, have become a mainstay in computational protein structure prediction performing among the best tools available. The quest for high quality generalized CG models presents an extremely challenging yet popular endeavor. To this point, a CG based interaction potential is presented here for the naturally occurring amino acids. In the present approach, three to four heavy atoms and associated hydrogens are condensed into a single CG site. The parametrization of the site-site interaction potential relies on experimental data thus providing a novel approach that is neither based on all-atom (AA) simulations nor experimental protein structural data. Specifically, intermolecular potentials, which are based on Lennard-Jones (LJ) style functional forms, are parametrized using thermodynamic data including surface tension and density. Using this approach, an amino acid potential data set has been developed for use in modeling peptides and proteins. The potential is evaluated here by comparing the solvent accessible surface area (SASA) to AA representations and ranking of protein decoy data sets provided by Decoys 'R' Us. The model is shown to perform very well compared to other existing prediction models for these properties.

Original languageEnglish
Pages (from-to)2115-2124
Number of pages10
JournalJournal of Chemical Theory and Computation
Volume5
Issue number8
DOIs
Publication statusPublished - Aug 2009
Externally publishedYes

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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