Customized versus universal scoring functions
Abstract
A tailor-made free energy scoring method (Fresno) has been compared to six universal scoring functions (Chemscore, Dock, FlexX, Gold, Pmf, Score) for predicting the binding affinity of 26 peptides to the class I human major histocompatibility protein HLA-B*2705. Fresno clearly outperforms all six universal scoring functions.
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Adapting the Fresno empirical scoring function to the class I MHC HLA-B*2705 protein significantly improved affinity prediction over six different traditional scoring functions.
“For instance, Logean et al. (2001) adapted the Fresno empirical scoring function to the class I MHC HLA-B∗2705 protein with a significant improvement in affinity prediction over six different traditional scoring functions.”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Logean et al., 2001
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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- Authors
- Logean, A., Sette, A., & Rognan, D.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Rognan, Didier
- Venue
- Bioorganic & Medicinal Chemistry Letters
- Publisher
- Elsevier BV
- Published
- 2001-03
- Volume
- 11
- Issue
- 5
- Pages
- 675-679
- ISSN
- 0960-894X (ISSN-L)
- OpenAlex
- W156083275
- Cited by
- 46
- References
- 24
- Citations by year
- 2024: 1 · 2021: 2 · 2020: 1 · 2018: 2 · 2016: 2 · 2015: 1 · 2013: 6
- FWCI
- 4.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioorganic & Medicinal Chemistry Letters (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- National Institute of Allergy and Infectious Diseases (AI9563)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- binding affinity prediction, peptide-MHC binding, HLA-B*2705, MHC class I, Fresno, protein-ligand docking, peptide ligands
- MeSH terms
- Binding Sites, Antibody, Humans, Ligands, Models, Molecular, Peptides, Protein Binding, Protein Conformation, Thermodynamics, HLA-B Antigens, Crystallography, X-Ray
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