The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
Open accessAbstract
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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“These datasets have been widely used to test the predictive power of the PPI prediction methods [12, 13, 27–29, 29–35].”
From Deep geometric representations for modeling effects of mutations on protein-protein binding affinity (2021) · cites this paper as [28]
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DESPOT: Direction-Enhanced Scoring POTentials for Scoring of Protein–Ligand Interactions
Poelmans, R., Eynde, W. V., Shemy, A., Bruncsics, B., Arany, Á., Moreau, Y., & Voet, A. R. D. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c02173
Metadata
- Authors
- Zhou, H., & Zhou, Y.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Zhou, Yaoqi
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2002-11
- Volume
- 11
- Issue
- 11
- Pages
- 2714-2726
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- 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
- 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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