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Bioinformatics Advance Access published online on October 21, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp599
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Jian Yu 1, Yong Zhou 1, Isao Tanaka 1 and Min Yao 1,*

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

*To whom correspondence should be addressed. Prof. Min Yao, E-mail: yao{at}castor.sci.hokudai.ac.jp


  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

Contact: yao{at}castor.sci.hokudai.ac.jp

Associate Editor: Prof. Anna Tramontano

Received on August 13, 2009; revised on September 26, 2009; accepted on October 9, 2009

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