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

ABSTRACT:

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.

SUBMITTER: Saberi Fathi SM 

PROVIDER: S-EPMC4112621 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature