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PMID: 12381853 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction.

Protein science : a publication of the Protein Society ·Vol. 11 ·No. 11 ·2002-11-00 ·Pages 2714-26

Zhou H, Zhou Y

Abstract

The distance-dependent structure-derived potentials developed so far all employed a reference state that can be characterized as a residue (atom)-averaged state. Here, we establish a new reference state called the distance-scaled, finite ideal-gas reference (DFIRE) state. The reference state is used to construct a residue-specific all-atom potential of mean force from a database of 1011 nonhomologous (less than 30% homology) protein structures with resolution less than 2 A. The new all-atom potential recognizes more native proteins from 32 multiple decoy sets, and raises an average Z-score by 1.4 units more than two previously developed, residue-specific, all-atom knowledge-based potentials. When only backbone and C(beta) atoms are used in scoring, the performance of the DFIRE-based potential, although is worse than that of the all-atom version, is comparable to those of the previously developed potentials on the all-atom level. In addition, the DFIRE-based all-atom potential provides the most accurate prediction of the stabilities of 895 mutants among three knowledge-based all-atom potentials. Comparison with several physical-based potentials is made.

MeSH Terms
Computational Biology Mathematics Models, Theoretical Protein Conformation Protein Folding Proteins/chemistry Statistics as Topic Thermodynamics
Chemicals
Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Zhou Hongyi
Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology & Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA.
Zhou Yaoqi
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Article Info
Journal
Protein science : a publication of the Protein Society
Abbr.
Protein Sci
ISSN
0961-8368
DOI
10.1110/ps.0217002
Published
2002-11-00
Pages
2714-26
Language
English
Region
United States
NLM ID
9211750
PMCID
PMC2373736
Subset
IM
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1110/ps.0217002 PMC Full Text View journal details
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