Table 1. Summary of some datasets of models in ModBase.

Dataset	Number of sequences attempted to be modeled	Number of sequences with reliable fold assignments	Number of models	Access
TrEMBL (2000)	415 801	197 999	371 816	Academic
TrEMBL (2001)	539 171	304 517	625 739	Academic
Homo sapiens	33 093	19 437	53 965
Mus musculus	20 792	11 772	32 138
Drosophila melanogaster	16 567	8692	27 240
Caenorhabditis elegans	19 326	9538	26 083
Arabidopsis thaliana	29 213	16 052	41 164
Saccharomyces cerevisiae	6714	2972	7218
Escherichia coli	13 787	6336	11 572
Mycoplasma genitalium	564	285	533
MODWEB	∼4500	3994	5140	Private
NYSGRC	13 451	7956	27 886	NYSGRC
Drosophila melanogaster*	21 225	7112	200 153	Academic
Saccharomyces cerevisiae ribosome	109	80	221	Academic

The number of sequences attempted to be modeled indicates the number of original sequences submitted to MODPIPE. For a definition of a reliable fold assignment see ‘Contents’. The number of models can be larger than the number of sequences because different segments of a sequence may be modeled independently and because the same segment may be modeled based on different template structures. The two TrEMBL datasets correspond to the June 2000 and March 23, 2001 versions of the complete TrEMBL database, respectively. For the 2001 TrEMBL dataset, the numbers for several organisms are shown separately. These numbers correspond to all the entries in the TrEMBL database, including multiple submissions, mutants and partial sequences. The MODWEB datasets are created by the MODWEB comparative modeling web server (http://guitar.rockefeller.edu/modweb) (N.Eswar and A.Sali, manuscript in preparation). The NYSGRC datasets are used in target selection and structure-based annotation by NYSGRC (37). The D.melanogaster* dataset contains models for the over-predicted putative genes in the D.melanogaster genome (38). The S.cerevisiae ribosome dataset contains comparative models for proteins in the yeast ribosome (40).