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: October 20th, 2016.

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: September 13th, 2016.

uniprot90.gz (3.9GiB download; file size 4146053389 bytes; MD5 sum b595e3c2710c80217a3f91ad3a506023)

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: October 20th, 2016.

20161020_pdb95_profiles.tar.bz2 (37GiB download; file size 38716358351 bytes; MD5 sum 44702492f882f194e8c7a7dd7b3c38c7)

20161020_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 However, much of it is out of date; many of the examples will not work with recent Modeller versions.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.