PDB-2-PBv2.0
Developed by V. Suresh, X. Zhou and S. Parthasarathy*
* For correspondence bdupartha@gmail.com

PDB-2-PB[1] is a curated online Protein Block (PB) sequence database. Here, we encoded and provide the PB sequences for all the protein structures available in PDB using de Brevern[2], encoding procedure. From our PDB-2-PB, users can extract the PB sequences along with their corresponding information as follows; (i) amino acid sequence, (ii) chain length, (iii) sequence start and end positions, (iv) resolution (only for X-ray solved entries), (v) experimental method used, and (vi) dihedral angles (φ and ψ), which we used to assign PB letters.

Description of PB. Details for PB letters a to p, are available here. For more details about PBs, click here

Statistics. Detailed statistics for all the versions of PDB-2-PB is available here.

A sample PDB-2-PB record. To view a sample record from our PDB-2-PB, click here.

Extracting the PB sequence from PDB-2-PB.

Mirror Site. Mirror Site for our PDB-2-PB is also available here.

Applications. Protein block sequences have many applications in protein structure analysis[3]. Our PB based protein fold recognition server PredictFold-PB[4] can also accessible here.

References

[1]  Suresh,V., Ganesan,K and Parthasarathy,S. (2012) PDB-2-PB: A curated online Protein Block Sequence Database. J. Appl. Cryst., 45, 127 -129.

[2] de Brevern,A.G., Etchebest,C and Hazout,S. (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins, 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. (2013) A protein block based fold recognition method for the annotation of twilight zone sequences. Protein and Peptide Lett., 20(3), 249-54.


Please, send your comments, suggestions to: bdubioserver@gmail.com


© 2014 - S. Parthasarathy, Bharathidasan University, India