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: March 29th, 2012.

• All PDB sequences:
  pdball.pir.gz
• Clustered at 95% identity:
  pdb_95.cod.gz (PDB codes of cluster representatives)
  pdb_95.grp.gz (PDB codes in each cluster)
  pdb_95.pir.gz (sequences of cluster representatives)

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: March 23rd, 2012.

uniprot90.gz (1.2G download; file size 1288128541 bytes; MD5 sum 5f0c2aac85a280bb38f74e84354c8710)

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: March 25th, 2012.

20120325_pdb95_profiles.tar.gz (18GB download; file size 18494203874 bytes; MD5 sum 5850a348a36328af4b57969f11d98062)

20120325_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 However, much of it is out of date; many of the examples will not work with recent Modeller versions.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 slides and example files for our 2010 MODELLER/IMP workshop in Erice, Sicily are available for download.

• All slides and example files for our 2010 CCPB/TYC IMP and MODELLER workshop are available for download.

• 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 Pages 97-129. Manuscript, and input/output files.

• Fiser, Do, and Sali. 2000. "Modeling of loops in protein structures". Protein Science 9, Pages 1753-1773. Loops (from 1 to 14 residues) used as the benchmark set.

• 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.