Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. - Inserm - Institut national de la santé et de la recherche médicale
Journal Articles Nucleic Acids Research Year : 2006

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

Abstract

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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Dates and versions

inserm-00133751 , version 1 (23-07-2007)

Identifiers

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Manoj Tyagi, Priyanka Sharma, C. S. Swamy, Frédéric Cadet, N. Srinivasan, et al.. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.. Nucleic Acids Research, 2006, 34 (Web Server issue), pp.W119-23. ⟨10.1093/nar/gkl199⟩. ⟨inserm-00133751⟩
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