Developed by V. Suresh, X. Zhou and S. Parthasarathy*
* For correspondence firstname.lastname@example.org
PDB-2-PB 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, 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.
1. Search PDBid for single PB sequenceMirror Site. Mirror Site for our PDB-2-PB is also available here.
2. Search parameter list for multiple PB sequences
3. Download multiple PB sequences for given PDBid list
Applications. Protein block sequences have many applications in protein structure analysis. Our PB based protein fold recognition server PredictFold-PB can also accessible here.
 Suresh,V., Ganesan,K and Parthasarathy,S. (2012) PDB-2-PB: A curated online Protein Block Sequence Database. J. Appl. Cryst., 45, 127 -129.
 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.
 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.
 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.
© 2014 - S. Parthasarathy, Bharathidasan University, India