Analysis of ligand binding sites using alpha shapes

Weiqiang Zhou, Hong Yan

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

Abstract

Protein-ligand interaction is important in drug development and protein design. Previous studies focused on the detection of the potential ligand binding sites but lack of analysis of the true binding sites on the protein. In this work, we use alpha shape models to represent the surface of the protein structure and extract surface patches to study the ligand binding sites. Analysis is performed on X-ray crystallography data of protein-ligand structures. The results show that geometric properties play a significant role in the positioning of ligand molecule in protein-ligand interaction.

Original languageEnglish (US)
Title of host publicationProceedings 2012 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2012
Pages536-540
Number of pages5
DOIs
StatePublished - Dec 1 2012
Externally publishedYes
Event2012 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2012 - Seoul, Korea, Republic of
Duration: Oct 14 2012Oct 17 2012

Publication series

NameConference Proceedings - IEEE International Conference on Systems, Man and Cybernetics
ISSN (Print)1062-922X

Other

Other2012 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2012
CountryKorea, Republic of
CitySeoul
Period10/14/1210/17/12

Keywords

  • Alpha shape models
  • protein-ligand interaction
  • solid angle
  • surface

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Control and Systems Engineering
  • Human-Computer Interaction

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