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Bioinformatics Advance Access originally published online on October 5, 2007
Bioinformatics 2007 23(24):3400-3402; doi:10.1093/bioinformatics/btm476
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Identification and visualization of cage-shaped proteins

Min Hu 1,*, Junhui Wang 2 and Qunsheng Peng 1

1State Key Laboratory of CAD & CG and 2College of Life Sciences, Zhejiang University, Hangzhou, 310058, China

*To whom correspondence should be addressed.


  Abstract

Summary: Cage-shaped protein, with its special structure, may have potential applications in biomedicine and nanotechnology. We developed a program CSPro (Cage-Shaped Protein) for efficient identification of cage-shaped proteins based on quaternary structure. CSPro is capable of revealing the corresponding cage-shaped feature more clearly and quickly than traditional visualization tools. Using CSPro, we have searched the full set of PDB (protein data bank) and three types of proteins are retrieved with notably large central cavities inside. CSPro can be used to validate if the quaternary structure of a protein is cage shaped in molecular simulation.

Availability: http://www.cad.zju.edu.cn/home/humin

Contact: humin{at}cad.zju.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on June 24, 2007; revised on September 4, 2007; accepted on September 17, 2007

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