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

Tyagi, M and Sharma, P and Swamy, CS and Cadet, F and Srinivasan, N and de Brevern, AG and Offmann, B (2006) Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. In: Nucleic Acids Research, 34 (Sp. Is). W119-W123.

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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/.

Item Type:	Journal Article
Publication:	Nucleic Acids Research
Publisher:	Oxford University Press
Additional Information:	Copyright of this article belongs to Oxford University Press.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	26 Aug 2010 07:35
Last Modified:	30 Jan 2012 06:39
URI:	http://eprints.iisc.ac.in/id/eprint/30555

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