Binding affinity analysis of protein-ligand complexes

Kai Cheng Hsu, Yen Fu Chen, Jinn Moon Yang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The prediction of the binding affinity of protein-ligand complexes is important for the molecular docking and rational drug discovery. In this study, we have analyzed the descriptors, which affect the binding affinities of protein-ligand complexes, from five dimensions, including protein-ligand interactions, protein properties, structural and physicochemical descriptors of ligands, metal-ligand bonding, and water effects. Based on these dimensions, we generated 87 descriptors and used stepwise regression to select seven of these descriptors to develop a new scoring function from 891 protein-ligand complexes. The seven selected descriptors include van der Waals contact, metal-ligand bonding, water effects, deformation penalties upon the binding process, and the number of highly conserved residues with hydrogen bonds. This new scoring function is evaluated on an independent set with 98 protein-ligand complexes and the correlation between predicted binding affinities and experimental values is 0.601. These results show that our new scoring function for the prediction of binding affinity is useful for molecular recognition and virtual screening for drug design.

Original languageEnglish
Title of host publication2nd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2008
PublisherIEEE Computer Society
Pages167-171
Number of pages5
ISBN (Print)9781424417483
DOIs
Publication statusPublished - 2008
Externally publishedYes
Event2nd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2008 - Shanghai, China
Duration: May 16 2008May 18 2008

Other

Other2nd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2008
CountryChina
CityShanghai
Period5/16/085/18/08

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Keywords

  • Binding affinity
  • Component
  • Drug design
  • Scoring function

ASJC Scopus subject areas

  • Biotechnology
  • Biomedical Engineering

Cite this

Hsu, K. C., Chen, Y. F., & Yang, J. M. (2008). Binding affinity analysis of protein-ligand complexes. In 2nd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2008 (pp. 167-171). [4534926] IEEE Computer Society. https://doi.org/10.1109/ICBBE.2008.46