Go to the abstract in the NAR 2002 Database Issue.
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http://guitar.rockefeller.edu/modbase
Pieper, U., Eswar, N., Stuart, A.C., Ilyin, V.A., Sali, A.
Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
Contact sali@rockefeller.edu
MODBASE (http://guitar.rockefeller.edu/ 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, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. 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.
Category Structure
Go to the abstract in the NAR 2002 Database Issue.