NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment

Abstract

The protein identification resource (PIR) and the Brookhaven National Laboratory protein data bank (PDB) are well-known databases for primary sequences and three-dimensional structures of proteins, respectively. Lesk et al, have compared the primary sequences in these two databases and concluded that the sequences in them are not redundant. Moreover, PIR programs can not be used directly on PDB files to access primary sequences because the FORMATS of these two data bases are different. We have developed a sequence-structure database, called NRL-3D, from the sequences, chain identification and the residue numbers of proteins in the PDB. This new database is designed such that it can be used in conjunction with PIR programs to search and extract sequences of interest and the corresponding three-dimensional coordinates from the structures in PDB.