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Nucleic Acids Research Advance Access originally published online on May 8, 2007
Nucleic Acids Research 2007 35(Web Server issue):W416-W419; doi:10.1093/nar/gkm228
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W416-W419
© 2007 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.

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3dLOGO: a web server for the identification, analysis and use of conserved protein substructures

Allegra Via1,*, Daniele Peluso1, Pier Federico Gherardini1, Emanuele de Rinaldis1,2, Teresa Colombo3,4, Gabriele Ausiello1 and Manuela Helmer-Citterich1

1Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, 2Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, 3Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and 4Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin

*To whom correspondence should be addressed. Tel: +39 067259 4324; Fax: +39 067259 4314; Email: allegra.via{at}uniroma2.it Correspondence may also be addressed to Manuela Helmer-Citterich. Email: citterich{at}uniroma2.it

Received December 21, 2006. Revised March 15, 2007. Accepted March 28, 2007.

3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/


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