ANNOUNCEMENT: ModBase database of comparative protein structure models

Tue Mar 16 09:47:10 EST 1999

ModBase database of comparative protein structure models
Roberto Sanchez and Andrej Sali 


ModBase is a queryable database of many annotated comparative protein
structure models. The models consist of coordinates for all non-hydrogen
atoms in the modeled part of a protein. They are derived by an automated
modeling pipeline relying mainly on the program MODELLER. The database
currently contains 3D models for substantial segments of 15-23% of proteins
in the genomes of M. genitalium, M. jannaschii, E. coli, S. cerevisiae,
and C. elegans. In total, there are models for 3,732 proteins. The
database also includes fold assignments and alignments on which the
models were based. In addition, special care is taken to assess the
overall quality of the models and their accuracy at the residue level.
In the future, ModBase will grow to reflect (i) the growth of the
sequence databases, (ii) the growth of the database of known protein
structures, (iii) and improvements in the software for calculating the
models. It is expected that the Swiss-Prot+TrEMBL protein sequence
database will be processed by the end of 1999. ModBase is introduced in 
R. Sanchez & A. Sali. Proc. Natl. Acad. Sci. USA 95, 13597-13602, 1998.

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