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: May 4th, 2017.

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: April 28th, 2017.

uniprot90.gz (5.0GiB download; file size 5306255684 bytes; MD5 sum 3db478c54a6d1f675ebe989d0476f6e5)

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: May 3rd, 2017.

20170503_pdb95_profiles.tar.bz2 (41GiB download; file size 43216493094 bytes; MD5 sum 3077c33dfc023a0df0566ad6d32916df)

20170503_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 However, much of it is out of date; many of the examples will not work with recent Modeller versions.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.