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Bioinformatics Advance Access published online on May 24, 2005
Bioinformatics, 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@oupjournals.org
Received March 23, 2005
Revised May 18, 2005
Accepted May 19, 2005

Applications note

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

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

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

* To whom correspondence should be addressed.
Sándor Pongor, E-mail: pongor{at}icgeb.org


  Abstract

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.

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


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