PDB-2-PB - BDU

PDB-2-PB^[1,2] 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^[3], 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 (), 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 Input/Output PDB-2-PB record. To view a sample Input/Output record Extracting the PB sequence from PDB-2-PB database with the following three options - HELP Page.

Extracting the PB sequence from PDB-2-PB

Applications. Protein block sequences have many applications in protein structure analysis^[4]. Our PB based protein fold recognition server PredictFold-PB^[5] can also accessible here.

References

[1] Muthuvel Prasath,K., Suresh,V. and Parthasarathy,S. (2020) PDB-2-PB.v3.0: An updated Protein Block database. Journal of Bioinformatics and Computational Biology. 18(2): 2050009.

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

[3] 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.

[4] 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.

[5] 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 Letters, 20(3), 249-254 .

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