ModBase

ModBase News

  • 4/20/2021: ModBase is now available only via HTTPS; old unencrypted HTTP connections will be automatically redirected.
  • 3/31/2021: Shorter URLs are now used for most top-level ModBase pages.
  • 7/24/2020: All ModBase models can now be downloaded in mmCIF format (in addition to PDB). mmCIF format has improved handling for large structures and can include multiple models in one file. All ModBase mmCIF files should be compliant with the PDBx and MA (Model Archive) dictionaries; see the wwPDB website for more information. Existing ModBase PDB files can be converted to mmCIF (they contain the same information) using utilities in the modbase_utils GitHub repository.
  • 5/18/2020: ModBase PDB files containing large residue numbers (>= 10,000) now use hybrid-36 notation to work around limitations of the traditional PDB format. This notation is supported by many PDB viewers, including Chimera and ChimeraX.
  • 7/19/2019: The web server account management system is now more flexible, and allows for forgotten passwords to be reset.
  • 7/10/2019: Most web services (such as ModLoop) have been modernized and now use the Flask framework.
  • 11/2/2016: The statistics page has been overhauled; older genome datasets are now hidden by default, links to downloads are provided, and PNG plots have been replaced with SVG.
  • 4/22/2013: Change in file download: coordinate files downloaded through the ModBase interface are now named by Model ID, or (if several coordinate files are bundled) as "modbase-models.pdb.xml"
  • 3/27/2013: ModPipe software update: the speed for individual sequence updates has decreased by 40% on average.
  • 2/28/2013: Check out our new website featuring the detailed results of a survey of the human transmembrane proteome: https://salilab.org/membrane.
  • 2/15/2013: Genome dataset update for Homo sapiens initiated. Completion is estimated for May 2013.
  • 12/18/2012: Weekly automatic modeling of new sequences in the SFLD database.
  • 2/27/2012: Genome dataset for Methanobrevibacter ruminantium M1 completed.
  • 2/25/2012: Nominate your genome! Email us at with suggestions for modelomes!
  • 2/15/2012: Genome dataset for Streptococcus mutans completed.
  • 1/13/2012: All files for selected full genome datasets are available at https://salilab.org/modbase-download/projects/genomes/.
  • 6/17/2011: Cavity information available through the Model Details page (see pull-down menu)
  • 6/17/2011: New, simplified Model Coverage Sketch
  • 9/15/2010: Check out the new UCSF Chimera - Modeller module for interactive modeling! (in the daily build)
  • 8/03/2010: Update trigger for individual sequences implemented
  • 8/02/2010: New Color-coding for quality criteria
  • 7/15/2010: ModBase facelift goes public
  • 7/14/2010: Genome dataset for Helicobacter pylori completed
  • 1/8/2010: Template Based modeling: New web-pages opened for template based statistics
  • 12/16/2009: ModWeb: New Frontend website with user registration and template based modeling