Data file downloads

Updated chains databases

These are the representative sequences derived from remediated PDB files. These files can be used to replace the various CHAINS_3.* files in the distributed Modeller's modlib directory if up to date chains files are desired. (Note that you can also build your own chains files if you have the PDB files available; see the example in the Modeller wiki.)

Last update: June 14th, 2018.

If for some reason you need databases of older (pre-remediation) PDB files, you can download them clustered at both 40% and 95% identity. (Last updated March 5th, 2007.)

Sequence database

This contains sequences from UniProt, clustered at 90% identity, in FASTA format.

Last update: June 10th, 2018.

uniprot90.gz (7.5GiB download; file size 7995073210 bytes; MD5 sum 8925cc9cdd4c16b43f5b67a2e87d3908)

Profile database

This contains profiles for sequences in PDB, clustered at 95% identity. Note that this is using the remediated PDB, unlike past releases.

Last update: June 14th, 2018.

20180614_pdb95_profiles.tar.bz2 (52GiB download; file size 55332399390 bytes; MD5 sum e9045db3f186845c8b6ab7f7711dd90b)

20180614_pdb95.pir.gz (Corresponding sequences)

Online material for past workshops and publications

Supplementary material is available for several of our past workshops and publications, and is provided here for completeness. However, much of it is out of date; many of the examples will not work with recent Modeller versions. You are recommended to use the tutorial instead.