MODBASE is a queryable database of annotated protein structure models. The models are derived by ModPipe, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database also includes the fold assignments and alignments on which the models were based. MODBASE contains theoretically calculated models, which may contain significant errors, not experimentally determined structures. Thus, special care is taken to assess the quality of the models. In addition to the protein structure models, MODBASE contains information about putative ligand binding sites, SNP annotation, and protein-protein interactions.