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

ModBase (http://salilab.org/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 (http://salilab.org/modeller/). 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 (http://salilab.org/modweb). ModBase models are available through the ModBase interface as well as the Protein Model Portal (http://www.proteinmodelportal.org/). Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment (http://salilab.org/salign), the ModEval server for predicting the accuracy of protein structure models (http://salilab.org/modeval), the PCSS server for predicting which peptides bind to a given protein (http://salilab.org/pcss) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (http://salilab.org/foxs).

Pubmed ID: 21097780


  • Pieper U
  • Webb BM
  • Barkan DT
  • Schneidman-Duhovny D
  • Schlessinger A
  • Braberg H
  • Yang Z
  • Meng EC
  • Pettersen EF
  • Huang CC
  • Datta RS
  • Sampathkumar P
  • Madhusudhan MS
  • Sj√∂lander K
  • Ferrin TE
  • Burley SK
  • Sali A


Nucleic acids research

Publication Data

January 23, 2011

Associated Grants

  • Agency: NIGMS NIH HHS, Id: F32 GM088991
  • Agency: NIGMS NIH HHS, Id: P01GM71790
  • Agency: NCRR NIH HHS, Id: P41RR001081
  • Agency: NIGMS NIH HHS, Id: R01 GM54762
  • Agency: NIGMS NIH HHS, Id: U01 GM61390
  • Agency: NIGMS NIH HHS, Id: U54 GM074929
  • Agency: NIGMS NIH HHS, Id: U54 GM074945
  • Agency: NIGMS NIH HHS, Id: U54GM074945

Mesh Terms

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