ModBase, a database of annotated comparative protein structure models and associated resources

Nucleic Acids Res. 2014 Jan;42(Database issue):D336-46. doi: 10.1093/nar/gkt1144. Epub 2013 Nov 23.


ModBase ( is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment ( ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server ( ModBase models are also available through the Protein Model Portal ( Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (, the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (, the FoXSDock server for protein-protein docking filtered by an SAXS profile (, the SAXS Merge server for automatic merging of SAXS profiles ( and the Pose & Rank server for scoring protein-ligand complexes ( In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Databases, Protein*
  • HIV Protease / chemistry
  • Humans
  • Internet
  • Membrane Proteins / chemistry
  • Models, Molecular*
  • Molecular Sequence Annotation
  • Protein Structure, Tertiary
  • Proteome / chemistry
  • Scattering, Small Angle
  • Structural Homology, Protein*
  • X-Ray Diffraction


  • Membrane Proteins
  • Proteome
  • HIV Protease
  • p16 protease, Human immunodeficiency virus 1