OPUS-Ca: A knowledge-based potential function requiring only Cα positions

Yinghao Wu, Mingyang Lu, Mingzhi Chen, Jialin Li, Jianpeng Ma

Research output: Contribution to journalArticle

63 Scopus citations

Abstract

In this paper, we report a knowledge-based potential function, named the OPUS-Ca potential, that requires only Cα positions as input. The contributions from other atomic positions were established from pseudo-positions artificially built from a Cα trace for auxiliary purposes. The potential function is formed based on seven major representative molecular interactions in proteins: distance-dependent pairwise energy with orientational preference, hydrogen bonding energy, short-range energy, packing energy, tri-peptide packing energy, three-body energy, and solvation energy. From the testing of decoy recognition on a number of commonly used decoy sets, it is shown that the new potential function outperforms all known Cα-based potentials and most other coarse-grained ones that require more information than Cα positions. We hope that this potential function adds a new tool for protein structural modeling. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)1449-1463
Number of pages15
JournalProtein Science
Volume16
Issue number7
DOIs
StatePublished - Jul 1 2007
Externally publishedYes

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Keywords

  • Decoy recognition
  • Knowledge-based potential function
  • Protein folding
  • Structure prediction

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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