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  1. PDB-REPRDB
    Resource Category : Databases -> Structure Databases -> Protein structure

    Brief Description : PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB) (1). Criteria used to select representatives are: a) quality of atomic co-ordinate data, b) sequence uniqueness, and c) conformation uniqueness. The system of PDB-REPRDB (2,3) is designed so that the user may obtain a quick selection of representative chains from PDB. System operation can be divided into two stages: 1) calculation of similarities between all pairs of protein chains, 2) classification of those chains and selection of representative chains according to priorities specified by the user. Similarities are calculated beforehand, and selection of representative chains can be dynamically configured according to the user\'s requirement. The WWW interface provides a large degree of freedom in setting parameters, such as cut-off scores of sequence and structural similarity. Users can eliminate unnecessary chains from the PDB chain list by setting threshold values and can also change priority of nine factors: resolution, R-factor, number of chain breaks, ratio of non-standard amino acid residues, ratio of residues with only Ca co-ordinates, ratio of residues with only backbone co-ordinates, number of residues, whether mutant or wild, and whether complex or not. Moreover, users can select whether or not to include entries by NMR experimental techniques and whether or not to include membrane protein chains by setting a flag of NMR and membrane, respectively. The membrane flag was introduced into the system in September 2002. One can obtain a representative list and classification data of protein chains from the system. The representative list includes information about factors mentioned above, EC number, and compound in PDB. The eIDf sections are hyper-linked to data on classified groups, and a graphic representation of three-dimensional structure can be displayed using the RasMol program by clicking on ef. Furthermore, eEcnumberf sections are hyper-linked to the Ligand chemical database for enzyme reactions (LIGAND) (4). The system is available at the new PDB-REPRDB WWW server (http://www.cbrc.jp/pdbreprdb/).

    Institute/s :
    National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan
    Address of Institute/s :
    National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan
    Country : Japan

    Associated Institutes :

    • Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan

    Associated Country : Japan


    Authors/Contributors : Tamotsu Noguchi; Yutaka Akiyama
    Contact Email : noguchi-tamotsu@aist.go.jp
    Year : 2002
    Language : English