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Bioinformatics Advance Access originally published online on May 24, 2005
Bioinformatics 2005 21(15):3322-3323; doi:10.1093/bioinformatics/bti513
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm

Zoltán Gáspári 1,2, Kristian Vlahovicek 3 and Sándor Pongor 1,3,*

1Bioinformatics Group, Biological Research Center, Hungarian Academy of Sciences Temesvári krt., 62, Szeged, Hungary
2Department of Organic Chemistry, Eötvös Loránd University Pázmány Péter sétány, 1/A, Budapest, Hungary
3Protein Structure and Bioinformatics, International Centre for Genetic Engineering and Biotechnology Area Science Park, Padriciano 99, 34012 Trieste, Italy

*To whom correspondence should be addressed.

Summary: An improved version of the PRIDE (PRobaility of IDEntity) fold prediction algorithm has been developed, based on more solid statistical basis, fast search capabilities and efficient input structure processing. The new algorithm is effective in identifying protein structures at the ‘H’ level of the CATH hierarchy.

Availability: The new algorithm is integrated into the PRIDE2 web servers at http://pride.szbk.u-szeged.hu and http://www.icgeb.org/pride

Contact: pongor{at}icgeb.org

Supplementary information: Detailed documentation and performance evaluation is available in the description section of the PRIDE2 web server.

Received on March 23, 2005; revised on May 18, 2005; accepted on May 19, 2005

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