Comparison of different ranking methods in protein-ligand binding site prediction.

ABSTRACT: In recent years, although many ligand-binding site prediction methods have been developed, there has still been a great demand to improve the prediction accuracy and compare different prediction algorithms to evaluate their performances. In this work, in order to improve the performance of the protein-ligand binding site prediction method presented in our former study, a comparison of different binding site ranking lists was studied. Four kinds of properties, i.e., pocket size, distance from the protein centroid, sequence conservation and the number of hydrophobic residues, have been chosen as the corresponding ranking criterion respectively. Our studies show that the sequence conservation information helps to rank the real pockets with the most successful accuracy compared to others. At t

SUBMITTER: Gao J 

PROVIDER: S-EPMC3430263 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature