PDB-2-PB: a curated online protein block sequence database

This article describes the development of a curated online protein block sequence database, PDB-2-PB. The protein block sequences for protein structures with complete backbone coordinates have been encoded using the encoding procedure of de Brevern, Etchebest & Hazout [Proteins (2000), 41, 271-287]. In the current release of the PDB-2-PB database (version 1.0), the protein entries from a recent release of the World Wide Protein Data Bank (wwPDB), which has 74 297 solved PDB entries as of 7 July 2011, have been used as a primary source. The PDB-2-PB database stores the protein block sequences for all the chains present in a protein structure. PDB-2-PB version 1.0 has the curated protein block sequences for 103 252 PDB chain entries (93 547 X-ray, 7033 NMR and 2672 other experimental chain entries). From the PDB-2-PB database, users can extract the curated protein block sequence and its corresponding amino acid sequence, which is extracted from the PDB ATOM records. Users can download these sequences either by using the PDB code or by using various parameters listed in the database. The PDB-2-PB database is freely available at http://bioinfo.bdu.ac.in/~pb/ .