Index of /modbase-download

[ICO]NameLast modifiedSizeDescription

[PARENTDIR]Parent Directory  -  
[   ]PrePPI_translation.txt.gz2012-10-30 13:57 908K 
[   ]ag2models.tar2018-05-26 09:23 1.0G 
[   ]agmodels.tar2018-05-02 17:51 797M 
[   ]aji_models.tar2020-06-11 18:38 31M 
[DIR]archive/2013-08-05 14:57 -  
[   ]me_models.tar2020-03-11 08:56 3.0G 
[   ]modbase_gi_sequenceID.txt.gz2020-09-24 16:42 1.8G 
[   ]modbase_models.latest2012-09-28 12:24 436M 
[   ]modbase_models.pmp.latest.gz2020-09-24 16:44 1.0G 
[   ]modbase_models_academic-20120928.txt.gz2012-09-28 12:24 436M 
[   ]modbase_models_all-20121111.txt.gz2012-11-12 00:44 2.4G 
[   ]modbase_models_all-20140226.txt.xz2014-02-28 10:53 2.2G 
[   ]modbase_models_all-latest.xz2014-02-28 10:53 2.2G 
[   ]modbase_models_pmp-20200910.txt.gz2020-09-10 16:23 1.0G 
[   ]modbase_models_pmp-20200917.txt.gz2020-09-17 16:07 1.0G 
[   ]modbase_models_pmp-20200924.txt.gz2020-09-24 16:44 1.0G 
[   ]modbase_pir-20090424.txt.gz2009-04-29 13:40 22M 
[   ]modbase_uniprot_rs-dbsnp.20061211.txt.gz2006-12-12 17:19 3.2M 
[TXT]modbase_uniprot_rs-dbsnp.txt2006-12-12 17:19 3.2M 
[   ]modpipe_pir.latest2009-04-29 13:40 22M 
[DIR]projects/2018-11-20 16:02 -  
[   ]rokaitis_models.tar2020-07-24 00:56 27G 
[   ]vtlmodels.tar2018-05-15 15:16 1.6G 
[   ]wdsp_models.tar2017-09-18 09:54 3.9M 
[   ]yao2_models.tar2017-08-15 22:27 1.1M 
[   ]yao_models.tar2017-08-10 10:53 242M 

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_".
ModBase mmCIF files contain data fields from the PDBx and MA (Model Archive)
dictionaries; see http://mmcif.wwpdb.org/ for more information.