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  1. ModBase
    Resource Category : Databases -> Structure Databases -> Protein structure

    Brief Description : MODBASE ( is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 415,937 out of 733,239 unique protein sequences in the complete TrEMBL database (March 2002); only models based on significant alignments (PSI-BLAST E-value < 10-4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling Web server.

    Institute/s :
    University of California at San Francisco, 1700 4th Street, San Francisco, CA
    Address of Institute/s :
    University of California at San Francisco, 1700 4th Street, San Francisco, CA
    Country : California

    Associated Institutes :

    • Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158
    • Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA
    • Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
    • Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigacion Principe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain
    • Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA

    Associated Country : USA; Spain

    Authors/Contributors : Ursula Pieper; Narayanan Eswar; Ben M. Webb; David Eramian; Libusha Kelly; David T. Barkan; Hannah Carter; Parminder Mankoo; Rachel Karchin; Marc A. Marti-Renom; Fred P. Davis; Andrej Sali
    Contact Email :
    Year : 2008
    Language : English