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

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Zhou, Hongyi, Zhou, Yaoqi·2002·Protein Science

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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.

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Authors: Zhou, H., & Zhou, Y.
Affiliations: Howard Hughes Medical Institute (US)
Corresponding author: Zhou, Yaoqi
ORCID: Zhou, Hongyi
Zhou, Yaoqi
Venue: Protein Science
Publisher: Wiley
Published: 2002-11
Volume: 11
Issue: 11
Pages: 2714-2726
ISSN: 0961-8368 (ISSN-L)
1469-896X
DOI: 10.1110/ps.0217002
PMC: PMC2373736
OpenAlex: W2125677968
Cited by: 902
References: 62
Citations by year: 2026: 10 · 2025: 15 · 2024: 15 · 2023: 23 · 2022: 20 · 2021: 34 · 2020: 34 · 2019: 44 · 2018: 40 · 2017: 48 · 2016: 37 · 2015: 45 · 2014: 64 · 2013: 64 · 2012: 49
FWCI: 5.58
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor, 2355 d)
Locations: Protein Science (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Howard Hughes Medical Institute
State University of New York
University at Buffalo
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Keywords: knowledge-based potentials, protein structure prediction, protein stability prediction, protein mutants, protein structure database
MeSH terms: Mathematics, Models, Theoretical, Protein Conformation, Proteins, Statistics as Topic, Thermodynamics, Protein Folding, Computational Biology

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

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