Data file downloads

Updated chains databases

These are the representative sequences derived from PDB files at 40% and 95% sequence identity. All X-ray and NMR PDB chains, with no limits on resolution, that are at least 30aa long, have at least 30 standard residues and not more than 10 non-standard residues were used to build these files.

Last update: March 5th, 2007.

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.)

All PDB sequences:
pdball.pir.gz
Clustered at 95% identity:
pdb_95.cod.gz pdb_95.grp.gz
Clustered at 40% identity:
pdb_40.cod.gz pdb_40.grp.gz

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: December 5th, 2007.

20071205_pdb95_profiles.tar.gz (5.3GB download; file size 5631824295 bytes; MD5 sum 24f3ad163de740e37d480a64d7c44024)

20071205_pdb95.pir (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 However, much of it is out of date; many of the examples will not work with recent Modeller versions.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.

All files used in our recent workshop in Uppsala, Sweden are available for download.
Sanchez and Sali. 2000. "Comparative protein structure modeling: Introduction and practical examples with MODELLER". Protein Science Prediction: Methods and Protocols (2000) Pages 97-129. Manuscript, and input/output files.
Fiser and Sali. 2003. "Comparative Protein Structure Modeling with MODELLER: A Practical Approach". Methods in Enzymology (2003) 374, Pages 463-493. Online text, and input/output files.
Manuscript by Marti-Renom, Fiser, Madhusudhan, John, Stuart, Eswar, Pieper, Shen and Sali. 2003. "Modeling Protein Structure From Its Sequence". Current Protocols in Bioinformatics (2003). V.5 November Issue, Pages 5.1.1-5.1.32. Files used in the "Example Of Comparative Modeling" section, updated for Modeller 7v7, are also available.