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  1. iProClass (View Publication)
    Full Name of the Resource : Integrated protein classification database
    Resource Category : Databases -> Protein Sequence Databases -> Protein Domain Databases (Protein Classification)

    Brief Description : The iProClass database provides an integrated view of protein information (Huang et al., 2003) and serves as a bioinformatics framework for data integration and associative analysis of proteins (Wu et al., 2004). iProClass presents value-added descriptions of all proteins in UniProtKB and contains comprehensive, up-to-date protein information derived from over 90 biological databases. Rich links to the underlying sources are provided with source attribution, hypertext links, and extracted summary information. The source databases include those of protein sequence, family, function, pathway, protein-protein interaction, complex, post-translational modification, protein expression, structure and structural classification, gene and genome, gene expression, disease, ontology, literature, and taxonomy. The iProClass protein summary report contains: (i) General information: protein ID and name (with synonyms, alternative names), source organism taxonomy (with NCBI taxonomy ID, group, and lineage), and sequence annotations such as gene names, keywords, function, and complex; (ii) Database cross-references: bibliography (with PubMed ID and link to a bibliography information and submission page), gene and genome databases including RefSeq, Entrez gene, gene ontology (with GO hierarchy and evidence tag), enzyme/function (with EC hierarchy, nomenclature and reaction), pathway (with KEGG pathway name and link to pathway map), protein-protein interaction, structure (with PDB 3D structure image, matched residue range, and % sequence identity for all structures matched at >=30% identity), structural classes (with SCOP hierarchy for structures at >=90% identity), sequence features and post-translational modifications (with residues or residue ranges); (iii) Family classification: PIRSF family, InterPro family, Pfam domain (with residue range), Prosite motif (with residue range), COG, and other classifications; and (iv) Sequence display: graphical display of domains and motifs on the amino acid sequence. iProClass is implemented in Oracle 9i database management system, updated biweekly, and searchable by both sequence and text. The data integration in iProClass allows identification of interesting relationships between protein sequence, structure, and function. It supports analyses of proteins in a "systems biology" context and has led to novel functional inference for uncharacterized proteins in the absence of sequence homology (Huang et al., 2005).
    Subject Area : Integrated Protein Classification


    Institute/s :
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057
    National Biomedical Research Foundation, Washington, DC 20057

    Address of Institute/s :
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057
    National Biomedical Research Foundation, Washington, DC 20057

    Country : United States

    Associated Institutes :

    • Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA
    • National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA

    Associated Country : USA


    Authors/Contributors : Wu, C.H.
    Contact Email : wuc@georgetown.edu
    Year : 2003
    Language : English

    Keywords : Amino Acid Sequence; Computational Biology; Databases, Factual; Genome, Human; Humans; Molecular Biology / methods; Molecular Sequence Data; Phosphoglycerate Mutase / chemistry / genetics / metabolism; Phylogeny; Proteins / chemistry / genetics / metabolism