 Developed by V. Suresh, K.Ganesan and S. Parthasarathy* Dept. of Bioinformatics, Bharathidasan University, Tiruchirappalli 620 024, India * For correspondence bdupartha@gmail.com
PDB-2-PB[1] is a curated online Protein Block (PB) sequence database. We have encoded the protein block sequences for the protein structures with complete backbone coordinates using the de Brevern[2], encoding procedure. From our PDB-2-PB database, an user can extract the curated protein block sequence of a chain along with its following corresponding information, (i) amino acid sequence, (ii) chain length, (iii) sequence start and end positions, (iv) resolution (only for X-ray solved entries), (v) the experimental method used, and (vi) dihedral angles (φ and ψ), which is used for assigning the PB letters. Users can extract these information using the following user friendly sequence retrieval system. Description of PB. Details of PB letters a to p, are available here. To know more details about the PB, click here Statistics. The detailed list of the PDB entries used and the curated PDB chain entries included in our PDB-2-PB database version 1.0, is available here. A sample PDB-2-PB record. To get a sample record from PDB-2-PB, click here. Extracting the PB sequence from PDB-2-PB.
1. Extract single PB sequence using a given PDB ID
Applications.
Protein block sequences have many applications in protein structure analysis[3]. We have also developed a protein fold recognition server PredictFold-PB[4], to predict the possible fold of a given Twilight Zone protein sequence.2. Extract multiple PB sequences using a given parameter list References [1] Suresh,V., Ganesan,K and Parthasarathy,S. (2011) PDB-2-PB: A curated online Protein Block Sequence Database. J. Appl. Cryst. (2012). 45 [2] de Brevern,A.G., Etchebest,C and Hazout,S. (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Protein s, 41, 271-287. [3] Joseph,A.P., Agarwal,G., Mahajan,S., Gelly,J.C., Swapna,L.S., Offmann,B., Cadet,F., Bornot,A., Tyagi,M., Valadié,H., Schneider,B., Etchebest,C., Srinivasan,N and de Brevern,A.G. (2010) A short survey on Protein Blocks. Biophysical Reviews, 2(3), 137-145. [4] Suresh,V., Ganesan,K and Parthasarathy,S. (2011) PredictFold-PB: A Protein Block based Fold Recognition Server for the Annotation of Twilight Zone Sequences. Protein and Peptide Letters. in press.
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