PBE – Protein Blocks Expert 2.0

PBE server 2.0 aims to provide a platform for protein structure analysis and comparison using well defined library of short structural motifs (SSMs) known as structural alphabets (SA). It uses a set of 16 SSMs called Protein Blocks (PBs) and a PB substitution matrix derived from large set of structurally aligned homologous proteins present in PALI database.

PBE international development team is composed of : Swapnil Mahajan, Manoj Tyagi, Priyanka Sharma, Murielle Grondin, Matthieu Drula, Aurore Vaïtinadapoullé, Etienne Frumence, Frédéric Cadet, N. Srinivasan, Alexandre G. de Brevern and Bernard Offmann and is developed jointly with PEACCEL Inc.

Features

• • PBE-T – Transformation of protein structure 3D information into 1D sequence of PBs

Protein structure comparison

• PB-ALIGNc – Structure comparison tool to identify local or global structural similarities between two protein structures
• PB-ALIGNm – Structure mining tool to identify proteins with similar fold from structural database given a query structure
• iPBA – also kindly consider to use iPBA server which has strong improvements with respects to PB-ALIGN. The algorithm search of anchors regions.
• mulPBA – Multiple alignment using protein blocks. It extends the method behind iPBA to multiple structural alignments.

• PBE-PENTAdb – A database for analysis of structural diversity of pentpeptides in terms of PBs
• PBE-kPRED – Knowledge-based tool for predicting local structure in terms of PBs
• PBE-PB-SVindex – structural diversity of pentapeptides in protein structures.
• DoSA – Database of structural alignments of structurally variable regions (currently unavailable)
• FoRSA – Protein fold recognition using protein blocks

References

1. Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre G. de Brevern and Narayanaswamy Srinivasan. DoSA: Database of Structural Alignments. Database (2013).
2. Swapnil Mahajan, Alexandre G. de Brevern, Bernard Offmann and Narayanaswamy Srinivasan. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. Journal of Biomolecular Structure & Dynamics (2013), in press.
3. Gelly JC, Joseph AP, Srinivasan N, de Brevern AG. iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucleic Acids Res. 2011, 39(Web Server issue):W18-23.
4. Agnel Praveen Joseph, Garima Agarwal, Swapnil Mahajan, Jean-Christophe Gelly, Lakshmipuram S. Swapna, Bernard Offmann, Frédéric Cadet, Aurélie Bornot, Manoj Tyagi and Hélène Valadié, et al. A short survey on protein blocks. Biophysical Reviews (2010) 2(3):137-145
5. Protein short loop prediction in terms of a structural alphabet. Tyagi M, Bornot A, Offmann B, de Brevern AG. Comput Biol Chem. (2009) 33(4):329-33.
6. Tyagi M., de Brevern A.G., Srinivasan N., Offmann B. Protein structure mining using a structural alphabet. Proteins 71:920–937, (2008).
7. Offmann B., Tyagi M., de Brevern A.G. Local Protein Structures. Current Bioinformatics, 2, 165-202, 2007.
8. Tyagi M, Gowri V.S., Srinivasan N,  de Brevern A.G, & Offmann B. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications. Proteins 65(1) :32-39, (2006).
9. Tyagi M, Sharma P, Swamy C.S, Cadet F, Srinivasan N, de Brevern A.G. and Offmann B. Protein Block Expert (PBE). A web-based protein structure analysis server using a structural alphabet. Nucleic Acids Res., 34:W119-W123, (2006).
10. de Brevern A.G. New assessment of a structural alphabet. In Silico Biology, 5, 26, (2005).
11. de Brevern A.G, Etchebest C. and Hazout S. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 41:271-287, (2000).

–>