Showing Publication Results for :

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

  1. Title of the Paper : iProClass: an integrated database of protein family, function and structure information (View at PubMed)
    Contributors : Huang, H.; Barker, W. C.; Chen, Y.; Wu, C. H.
    Address : Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA.
    Publication Name : Nucleic Acids Res
    Volume : 31
    Issue : 1
    Pages : 390-2
    Publication Year : 2003
    ISSN : 1362-4962 (Electronic) 0305-1048 (Linking)
    Language : English
    Abstract : The iProClass database provides comprehensive, value-added descriptions of proteins and serves as a framework for data integration in a distributed networking environment. The protein information in iProClass includes family relationships as well as structural and functional classifications and features. The current version consists of about 830 000 non-redundant PIR-PSD, SWISS-PROT, and TrEMBL proteins organized with more than 36 000 PIR superfamilies, 145 000 families, 4000 domains, 1300 motifs and 550 000 FASTA similarity clusters. It provides rich links to over 50 database of protein sequences, families, functions and pathways, protein-protein interactions, post-translational modifications, protein expressions, structures and structural classifications, genes and genomes, ontologies, literature and taxonomy. Protein and superfamily summary reports present extensive annotation information and include membership statistics and graphical display of domains and motifs. iProClass employs an open and modular architecture for interoperability and scalability. It is implemented in the Oracle object-relational database system and is updated biweekly. The database is freely accessible from the web site at and searchable by sequence or text string. The data integration in iProClass supports exploration of protein relationships. Such knowledge is fundamental to the understanding of protein evolution, structure and function and crucial to functional genomic and proteomic research.

  2. Title of the Paper : iProClass: an integrated, comprehensive and annotated protein classification database (View at PubMed)
    Contributors : Wu, C. H.; Xiao, C.; Hou, Z.; Huang, H.; Barker, W. C.
    Address : Protein Information Resource, National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW Washington, DC 20007-2195, USA.
    Publication Name : Nucleic Acids Res
    Volume : 29
    Issue : 1
    Pages : 52-4
    Publication Year : 2001
    ISSN : 1362-4962 (Electronic) 0305-1048 (Linking)
    Language : English
    Abstract : The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200,000 non-redundant PIR and SWISS-PROT proteins organized with more than 28,000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at

  3. Title of the Paper : The iProClass integrated database for protein functional analysis (View at PubMed)
    Contributors : Wu, C. H.; Huang, H.; Nikolskaya, A.; Hu, Z.; Barker, W. C.
    Address : Georgetown University Medical Center, Washington, DC 20057-1455, USA.
    Publication Name : Comput Biol Chem
    Volume : 28
    Issue : 1
    Pages : 87-96
    Publication Year : 2004
    ISSN : 1476-9271 (Print) 1476-9271 (Linking)
    Language : English
    Abstract : Increasingly, scientists have begun to tackle gene functions and other complex regulatory processes by studying organisms at the global scales for various levels of biological organization, ranging from genomes to metabolomes and physiomes. Meanwhile, new bioinformatics methods have been developed for inferring protein function using associative analysis of functional properties to complement the traditional sequence homology-based methods. To fully exploit the value of the high-throughput system biology data and to facilitate protein functional studies requires bioinformatics infrastructures that support both data integration and associative analysis. The iProClass database, designed to serve as a framework for data integration in a distributed networking environment, provides comprehensive descriptions of all proteins, with rich links to over 50 databases of protein family, function, pathway, interaction, modification, structure, genome, ontology, literature, and taxonomy. In particular, the database is organized with PIRSF family classification and maps to other family, function, and structure classification schemes. Coupled with the underlying taxonomic information for complete genomes, the iProClass system ( supports associative studies of protein family, domain, function, and structure. A case study of the phosphoglycerate mutases illustrates a systematic approach for protein family and phylogenetic analysis. Such studies may serve as a basis for further analysis of protein functional evolution, and its relationship to the co-evolution of metabolic pathways, cellular networks, and organisms.