Index of /modbase-download
The following files with ModBase metadata are available:
modbase_gi_sequenceID.txt.gz: Mapping from database identifiers (such as GI
numbers) to ModBase sequence IDs.
modbase_models.pmp.latest.gz: Only the newest dataset for each ModBase sequence,
no external database ids (redundancy removed). 16 million entries,
modbase_models_all-latest.xz: All ModBase models, but only for current UniProt
IDs. 21 million entries, updated infrequently
modbase_models.latest: All ModBase models, for all UniProt IDs in the database.
49 million entries, updated infrequently
For downloadable models of genome calculations, see:
To download individual model files, a couple of options are available.
Please don't try to download the whole ModBase database using the command-line
option (wget or curl, see below). Send an email to firstname.lastname@example.org if you
are interested in downloading a large number of models. Attach a list of the
ModBase model IDs (not database IDs) you want. These can be determined using
some of the metadata files above such as modbase_gi_sequenceID.txt.gz and
modbase_models.pmp.latest.gz (or a ModBase sequence ID can be calculated directly
from the sequence, as the MD5 hash of the primary sequence without gaps or line
breaks, followed by the first 4 and last 4 residues, so that of
All models for a database ID:
curl -L "https://salilab.org/modbase/retrieve?databaseID=Q12321"
All models for a sequence ID:
curl -L "https://salilab.org/modbase/retrieve?seqID=16f39f89e31970dbec2f39c36959c116MVEGDIVS"
One specific model:
curl -L "https://salilab.org/modbase/retrieve?modelID=064dd62ea7483831c9cfc1f72499630e"
By default this will download models in PDB format in a single file, with
models separated by XML tags. To get files in mmCIF format instead, add
"&format=mmcif" to the end of the URL, e.g.:
curl -L "https://salilab.org/modbase/retrieve?databaseID=Q12321&format=mmcif"
Each model in an mmCIF file starts with a line "data_model_".
ModBase mmCIF files contain data fields from the PDBx and ModelCIF
dictionaries; see http://mmcif.wwpdb.org/ for more information.