Comparison of Different Ranking Methods in Protein-Ligand Binding Site Prediction

International Journal of Molecular Sciences

Jun Gao¹  Qi Liu¹  Hong Kang¹  Zhiwei Cao¹ 

[1] College of Life Science and Biotechnology, Tongji University, Shanghai 200092, China; E-Mails:

关键词: ranking aggregation;    protein-ligand binding site;    prediction;   

DOI  :  10.3390/ijms13078752

来源: mdpi

【 摘 要 】

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 the same time, the pocket size and the distance of binding site from the protein centroid are also found to be helpful. In addition, a multi-view ranking aggregation method, which combines the information among those four properties, was further applied in our study. The results show that a better performance can be achieved by the aggregation of the complementary properties in the prediction of ligand-binding sites.

【 授权许可】

CC BY   
© 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.