Posted by: shrikantmantri | October 25, 2009

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

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

Publication Date: 2009 Oct 21 PMID: 19846440
Authors: Yu, J. – Zhou, Y. – Tanaka, I. – Yao, M.
Journal: Bioinformatics

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@castor.sci.hokudai.ac.jp.

Posted via email from Sharing significant bytes —(Shrikant Mantri)

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