General Information
| Description | A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere |
| Homepage | http://altair.sci.hokudai.ac.jp/g6/Research/POCASA_e.html |
Publications
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
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.
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