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

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. doi: 10.1093/nar/gkq1091. Epub 2010 Nov 19.


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 10,355,444 reliable models for domains in 2,421,920 unique protein sequences. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server ( ModBase models are available through the ModBase interface as well as the Protein Model Portal ( Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment (, the ModEval server for predicting the accuracy of protein structure models (, the PCSS server for predicting which peptides bind to a given protein ( and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (

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

  • Bacterial Proteins / chemistry
  • Computer Graphics
  • Databases, Protein*
  • Models, Molecular*
  • Peptides / chemistry
  • Protein Interaction Mapping
  • Protein Structure, Tertiary*
  • Proteins / chemistry
  • Scattering, Small Angle
  • Sequence Alignment
  • Software
  • Structural Homology, Protein
  • User-Computer Interface
  • X-Ray Diffraction


  • Bacterial Proteins
  • Peptides
  • Proteins