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

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

Jian Yu  1 , Yong Zhou, Isao Tanaka, Min Yao
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Free article

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

Jian Yu et al. Bioinformatics. .
Free article

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.

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