Journal Article

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

Jian Yu, Yong Zhou, Isao Tanaka and Min Yao

in Bioinformatics

Volume 26, issue 1, pages 46-52
Published in print January 2010 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp599
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere

More Like This

Show all results sharing this subject:

  • Bioinformatics and Computational Biology

GO

Show Summary Details

Preview

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

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5540 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.