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Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

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Huang, Sheng-You, Grinter, Sam Z., Zou, Xiaoqin·2010·Physical Chemistry Chemical Physics
DOI 10.1039/c0cp00151aPMC PMC11103779
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Abstract

The scoring function is one of the most important components in structure-based drug design. Despite considerable success, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking. In this perspective, we have reviewed three basic types of scoring functions (force-field, empirical, and knowledge-based) and the consensus scoring technique that are used for protein-ligand docking. The commonly-used assessment criteria and publicly available protein-ligand databases for performance evaluation of the scoring functions have also been presented and discussed. We end with a discussion of the challenges faced by existing scoring functions and possible future directions for developing improved scoring functions.

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Authors
Huang, S.-Y., Grinter, S. Z., & Zou, X.
Affiliations
University of Missouri (US)
Corresponding author
Zou, Xiaoqin
ORCID
Venue
Physical Chemistry Chemical Physics
Publisher
Royal Society of Chemistry (RSC)
Published
2010
Volume
12
Issue
40
Pages
12899
ISSN
  • 1463-9076 (ISSN-L)
  • 1463-9084
DOI
10.1039/c0cp00151a
PMC
PMC11103779
OpenAlex
W2038542598
Cited by
508
References
133
Citations by year
2026: 27 · 2025: 34 · 2024: 33 · 2023: 34 · 2022: 45 · 2021: 44 · 2020: 31 · 2019: 34 · 2018: 30 · 2017: 22 · 2016: 37 · 2015: 34 · 2014: 42 · 2013: 27 · 2012: 20
FWCI
1.66
Type
journal article
Language
en
Open access
Locations
  • Physical Chemistry Chemical Physics (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institute of General Medical Sciences (R21GM088517)
Topics
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
Keywords
protein-ligand docking, scoring functions, knowledge-based scoring, consensus scoring, structure-based drug design, protein-ligand binding affinity prediction, benchmarking database
MeSH terms
Algorithms, Computer Simulation, Ligands, Protein Binding, Proteins, Drug Design

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