Protein loop selection using orientation-dependent force fields derived by parameter optimization

Shide Liang, Chi Zhang, Daron M. Standley

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

We used the orientation-dependent Optimized Side Chain Atomic eneRgy (OSCAR-o), derived in an early study, for protein loop selection. The prediction accuracy of OSCAR-o was better than that of physics-based force fields or statistical potential energy functions for both the RAPPER decoy set and the Jacobson decoy set. The native conformer was frequently ranked as lowest energy among the decoys. Furthermore, strong correlation was observed between the OSCAR-o score and the root mean square deviation (RMSD) from the native structure for energy-minimized decoys. In practical use, we applied OSCAR-o to rescore decoys generated by a widely used loop-modeling program, LOOPY. As a result, the mean RMSD values of top-ranked decoys were reduced by 0.3 Å for loop targets of seven to nine residues. We expect similar performance for OSCAR-o with other loop-modeling algorithms in the context of decoy rescoring. A loop selection program (OSCAR-ls) based on OSCAR-o is available at.

Original languageEnglish (US)
Pages (from-to)2260-2267
Number of pages8
JournalProteins: Structure, Function and Bioinformatics
Volume79
Issue number7
DOIs
StatePublished - Jul 2011

Keywords

  • Decoy ensembles
  • Knowledge-based potential
  • Loop prediction
  • OSCAR-ls
  • OSCAR-o
  • Protein modeling

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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