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,
updated weekly.

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:

https://salilab.org/modbase-download/projects/genomes/
https://salilab.org/modbase-download/projects/tdi/

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 modbase@salilab.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
https://www.uniprot.org/uniprot/Q12321.fasta is
16f39f89e31970dbec2f39c36959c116MVEGDIVS).

All models for a database ID:

https://salilab.org/modbase/retrieve?databaseID=database_id_from_summary_file
for example:
curl -L "https://salilab.org/modbase/retrieve?databaseID=Q12321"

All models for a sequence ID:

https://salilab.org/modbase/retrieve?seqID=sequence_id_from_summary_file
for example:
curl -L "https://salilab.org/modbase/retrieve?seqID=16f39f89e31970dbec2f39c36959c116MVEGDIVS"

One specific model:

https://salilab.org/modbase/retrieve?modelID=modelid_from_summary_file
for example:
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_<modelID>".
ModBase mmCIF files contain data fields from the PDBx and ModelCIF
dictionaries; see http://mmcif.wwpdb.org/ for more information.