Fast and accurate prediction of protein side-chain conformations

Shide Liang, Dandan Zheng, Chi Zhang, Daron M. Standley

Research output: Contribution to journalComment/debatepeer-review

31 Scopus citations

Abstract

We developed a fast and accurate side-chain modeling program [Optimized Side Chain Atomic eneRgy (OSCAR)-star] based on orientation-dependent energy functions and a rigid rotamer model. The average computing time was 18 s per protein for 218 test proteins with higher prediction accuracy (1.1% increase for χ 1 and 0.8% increase for χ 1+2) than the best performing program developed by other groups. We show that the energy functions, which were calibrated to tolerate the discrete errors of rigid rotamers, are appropriate for protein loop selection, especially for decoys without extensive structural refinement.

Original languageEnglish (US)
Article numberbtr482
Pages (from-to)2913-2914
Number of pages2
JournalBioinformatics
Volume27
Issue number20
DOIs
StatePublished - Oct 2011

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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