Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere

Jian Yu; Yong Zhou; Isao Tanaka; Min Yao

doi:10.1093/bioinformatics/btp599

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere

Bioinformatics. 2010 Jan 1;26(1):46-52. doi: 10.1093/bioinformatics/btp599. Epub 2009 Oct 21.

Authors

Jian Yu¹, Yong Zhou, Isao Tanaka, Min Yao

Affiliation

¹ Graduate School of Life Science, Hokkaido University, Kita-Ku Kita-10 Nishi-8, Sapporo 0600810, Japan.

PMID: 19846440
DOI: 10.1093/bioinformatics/btp599

Abstract

Motivation: Prediction of ligand binding sites of proteins is significant as it can provide insight into biological functions and reaction mechanisms of proteins. It is also a prerequisite for protein-ligand docking and an important step in structure-based drug design.

Results: We present a new algorithm, Roll, implemented in a program named POCASA, which can predict binding sites by detecting pockets and cavities of proteins with a rolling sphere. To evaluate the performance of POCASA, a test with the same data set as used in several existing methods was carried out. POCASA achieved a high success rate of 77%. In addition, the test results indicated that POCASA can predict good shapes of ligand binding sites.

Availability: A web version of POCASA is freely available at http://altair.sci.hokudai.ac.jp/g6/Research/POCASA_e.html.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Binding Sites
Computer Simulation
Models, Chemical*
Models, Molecular*
Protein Binding
Protein Interaction Mapping / methods*
Proteins / chemistry*
Proteins / ultrastructure*
Software*

Substances

Proteins