A simple method for finding a protein’s ligand-binding pockets

BMC Structural Biology

Jack A Tuszynski¹  Seyed Majid Saberi Fathi² 

[1] Department of Physics, University of Alberta, Edmonton, Alberta, Canada;Department of Physics, Ferdowsi University of Mashhad, Mashhad, Iran

关键词: Computational methods;    Ligand-binding pockets;    Protein structure;   

Others  :  1090799
DOI  :  10.1186/1472-6807-14-18

 received in 2014-01-09, accepted in 2014-07-11,  发布年份 2014

【 摘 要 】

Background

This paper provides a simple and rapid method for a protein-clustering strategy. The basic idea implemented here is to use computational geometry methods to predict and characterize ligand-binding pockets of a given protein structure. In addition to geometrical characteristics of the protein structure, we consider some simple biochemical properties that help recognize the best candidates for pockets in a protein’s active site.

Results

Our results are shown to produce good agreement with known empirical results.

Conclusions

The method presented in this paper is a low-cost rapid computational method that could be used to classify proteins and other biomolecules, and furthermore could be useful in reducing the cost and time of drug discovery.

【 授权许可】

   
2014 Saberi Fathi and Tuszynski; licensee BioMed Central Ltd.

【 图 表 】

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