Index of /ftp/databases/modbase

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[ ]modbase_models_all-20121111.txt.gz2012-11-12 00:44 2.4G 
[ ]modbase_models_all-latest.xz2014-02-28 10:53 2.2G 
[ ]modbase_models_all-20140226.txt.xz2014-02-28 10:53 2.2G 
[ ]modbase_gi_sequenceID.txt.gz2024-11-21 15:41 1.8G 
[ ]modbase_models_pmp-20241114.txt.gz2024-11-14 15:37 1.1G 
[ ]modbase_models_pmp-20241121.txt.gz2024-11-21 15:41 1.1G 
[ ]modbase_models.pmp.latest.gz2024-11-21 15:41 1.1G 
[ ]modbase_models_pmp-20241107.txt.gz2024-11-07 15:38 1.1G 
[ ]ag2models.tar2018-05-26 09:23 1.0G 
[ ]agmodels.tar2018-05-02 17:51 797M 
[ ]fcankara20.tar2024-04-15 18:19 753M 
[ ]aydin_table1.tar2022-11-07 14:53 458M 
[ ]modbase_models_academic-20120928.txt.gz2012-09-28 12:24 436M 
[ ]modbase_models.latest2012-09-28 12:24 436M 
[ ]aydin_table2.tar2022-11-07 14:53 372M 
[ ]modpipe_pir.latest2009-04-29 13:40 22M 
[ ]modbase_pir-20090424.txt.gz2009-04-29 13:40 22M 
[TXT]modbase_uniprot_rs-dbsnp.txt2006-12-12 17:19 3.2M 
[ ]modbase_uniprot_rs-dbsnp.20061211.txt.gz2006-12-12 17:19 3.2M 
[ ]PrePPI_translation.txt.gz2012-10-30 13:57 908K 
[DIR]projects/2018-11-20 16:02 -  
[DIR]archive/2013-08-05 14:57 -  
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 ModelCIF
dictionaries; see http://mmcif.wwpdb.org/ for more information.