MODBASE, a database of annotated comparative protein structure models

Abstract

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 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); 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.

Figure 1

Some MODBASE query and results pages. (A) Summary of search criteria. (B) Summary display of search results, either all models satisfying the search criteria or all sequences with models satisfying the search criteria. (C) Model display page shows a schematic alignment and some information either about all models of one sequence or about all models based on one template structure. (D) Sample window of MODVIEW, a Netscape plugin for displaying and analyzing multiple sequences and structures (http://guitar.rockefeller.edu/modview).