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Nucleic Acids Research Advance Access originally published online on May 6, 2008
Nucleic Acids Research 2008 36(Web Server issue):W42-W46; doi:10.1093/nar/gkn197
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W42-W46
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes

Roberto Mosca1,3 and Thomas R. Schneider1,2,3,*

1IFOM, the FIRC Institute for Molecular Oncology Foundation, Via Adamello 16, 20139, 2European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy and 3European Molecular Biology Laboratory Hamburg, c/o DESY Notkestrasse 85 22603 Hamburg, Germany

*To whom correspondence should be addressed. Tel: +49 40 89902 190; Fax: +49 40 89902 149; Email: thomas.schneider{at}embl-hamburg.de

Received January 31, 2008. Revised March 12, 2008. Accepted April 2, 2008.

Rapid alignment of proteins in terms of domains (RAPIDO) is a web server for the 3D alignment of crystal structures of different protein molecules in the presence of conformational change. The structural alignment algorithm identifies groups of equivalent atoms whose interatomic distances are constant (within a defined tolerance) in the two structures being compared and considers these groups of atoms as rigid bodies. In addition to the functionalities provided by existing tools, RAPIDO can identify structurally equivalent regions also when these consist of fragments that are distant in terms of sequence and separated by other movable domains. Furthermore, RAPIDO takes the variation in the reliability of atomic coordinates into account in the comparison of distances between equivalent atoms by employing weighting-functions based on the refined B-values. The regions identified as equivalent by RAPIDO furnish reliable sets of residues for the superposition of the two structures for subsequent detailed analysis. The RAPIDO server, with related documentation, is available at http://webapps.embl-hamburg.de/rapido.


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