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Nucleic Acids Research 2006 34(Web Server issue):W119-W123; doi:10.1093/nar/gkl199
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© The Author 2006. 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@oxfordjournals.org

Article

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

M. Tyagi1, P. Sharma1, C. S. Swamy2, F. Cadet1, N. Srinivasan1,2, A. G. de Brevern3 and B. Offmann1,*

1 Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La Réunion BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France 2 Molecular Biophysics Unit, Indian Institute of Science Bangalore 560 012, India 3 INSERM, U726, Equipe de Bioinformatique et Génomique Moléculaire (EBGM), Université Paris 7—Denis Diderot case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France

*To whom correspondence should be addressed. Tel: +262 262 93 8641; Fax: +262 262 93 8237; Email: bernard.offmann{at}univ-reunion.fr

Received February 14, 2006. Revised March 21, 2006. Accepted March 21, 2006.

Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/PBE/.


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