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

61 Citations (Scopus)

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 2007
Externally publishedYes

Fingerprint

Hydrogen Bonding
Proteins
Peptides
Molecular interactions
Solvation
Ports and harbors
Hydrogen bonds
Testing

Keywords

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

ASJC Scopus subject areas

  • Biochemistry

Cite this

OPUS-Ca : A knowledge-based potential function requiring only Cα positions. / Wu, Yinghao; Lu, Mingyang; Chen, Mingzhi; Li, Jialin; Ma, Jianpeng.

In: Protein Science, Vol. 16, No. 7, 07.2007, p. 1449-1463.

Research output: Contribution to journalArticle

Wu, Yinghao ; Lu, Mingyang ; Chen, Mingzhi ; Li, Jialin ; Ma, Jianpeng. / OPUS-Ca : A knowledge-based potential function requiring only Cα positions. In: Protein Science. 2007 ; Vol. 16, No. 7. pp. 1449-1463.
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