Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets.

ABSTRACT: Comprehensive analysis and comparison of protein ligand-binding pockets are important to predict the ligands which bind to parts of putative ligand binding pockets. Because of the recent increase of protein structure information, such analysis demands a fast and efficient method for comparing ligand binding pockets. Previously we proposed a fast alignment-free method based on a simple representation of a ligand binding pocket with one 11-dimensional vector, which is suitable for such analysis. Based on that method, we conducted this study to expand and revise similarity measures of binding pockets and to investigate the effects of those modifications with two datasets for improving the ability to detect similar binding pockets. The new method exhibits higher detection performance of simila

SUBMITTER: Nakamura T 

PROVIDER: S-EPMC5042158 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature