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  1. FireDB (View Publication)
    Full Name of the Resource : Functionally important residues in protein structures
    Resource Category : Databases -> Protein Sequence Databases -> Protein sequence motifs and active sites

    Brief Description : FireDB is a fully automated search system for structures in the Protein Data Bank(PDB), that contain annotations of residues participating in a functional site. The sources of functional residues are protein-ligand atom contacts and the Catalytic Site Atlas. The whole PDB was clustered at 97% sequence identity and every chain mapped onto a consensus (Master sequence) from the cluster, so that important positions can be mapped and binding sites collapsed into the master sequence. Comparison of binding sites within a cluster of sequences gives an idea of the flexibility of those regions and the capability they have to bind different ligand analogs. Another utility is the biological relevance assesment of small molecule binding sites found in the PDB structures. The Database can be accessed by PDB codes,Uniprot primary accession numbers or keywords as well as small molecule ligands. Molecular visualzationis is also available when navigating across FireDB.
    Subject Area : Protein Databank; Functional Site


    Institute/s :
    Spanish National Cancer Research Center, Structural and Computational Biology Program, Madrid, Spain
    Address of Institute/s :
    Spanish National Cancer Research Center, Structural and Computational Biology Program, C/ Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain
    Country : Spain

    Associated Institutes :

    • Computational and Structural Biology Program, Spanish National Cancer Research Centre (CNIO) Melchor Fern├índez Almagro, 3, E-28029, Madrid, Spain

    Associated Country : Spain


    Authors/Contributors : Gonzalo Lopez
    Contact Email : glopez@cnio.es
    Year : 2006
    Language : English

    Keywords : Amino Acids / chemistry; Binding Sites; Catalytic Domain; Databases, Protein; Internet; Ligands; Models, Molecular; Protein Conformation; Proteins / chemistry; Tacrolimus Binding Proteins / chemistry; User-Computer Interface