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Nucleic Acids Research, 2000, Vol. 28, No. 1 250-253
© 2000 Oxford University Press

MODBASE, a database of annotated comparative protein structure models

Roberto Sánchez, Ursula Pieper, Neboja Mirkovi, Paul I. W. de Bakker, Edward Wittenstein and Andrej ali*

Laboratories of Molecular Biophysics, The Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA

MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia coli, as well as all the available sequences from Arabidopsis thaliana and Homo sapiens. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the quality of the models. ModBase is accessible through a web interface at http://guitar.rockefeller.edu/modbase/

* To whom correspondence should be addressed. Tel: +1 212 327 7550; Fax: +1 212 327 7540; Email: sali@rockefeller.edu


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