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Nucleic Acids Research 2005 33(Web Server Issue):W252-W254; doi:10.1093/nar/gki362
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures

Kristian Vlahovicek, Alessandro Pintar, Laavanya Parthasarathi, Oliviero Carugo and Sándor Pongor*

Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology Area Science Park, 34012 Trieste, Italy

*To whom correspondence should be addressed. Fax: +39 04 226 555; Email: pongor{at}icgeb.org

Received February 1, 2005. Revised February 23, 2005. Accepted February 23, 2005.

The WWW servers at http://www.icgeb.org/protein/ are dedicated to the analysis of protein 3D structures submitted by the users as the Protein Data Bank (PDB) files. CX computes an atomic protrusion index that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index for the buried atoms and makes it possible to analyze the distribution of buried residues. CX and DPX return PDB files containing the calculated indices that can then be visualized using standard programs, such as Swiss-PDBviewer and Rasmol. PRIDE compares 3D structures using a fast algorithm based on the distribution of inter-atomic distances. The options include pairwise as well as multiple comparisons, and fold recognition based on searching the CATH fold database.

Present addresses: L. Parthasarathi, Department of Clinical Pharmacology, Royal College of Surgeons, Dublin 2, Ireland

O. Carugo, Department of General Chemistry, University of Pavia, 27100 Pavia, Italy


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