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

Academic Article
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Overview

authors

  • Pieper, U.
  • Webb, B. M.
  • Dong, G. Q.
  • Schneidman-Duhovny, D.
  • Fan, H.
  • Kim, S. J.
  • Khuri, N.
  • Spill, Y. G.
  • Weinkam, P.
  • Hammel, M.
  • Tainer, John
  • Nilges, M.
  • Sali, A.

publication date

  • 2014

journal

  • Nucleic Acids Research  Journal

abstract

  • 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 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 (http://salilab.org/modweb). ModBase models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein-protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein-ligand complexes (http://salilab.org/poseandrank). 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.

subject areas

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

PubMed Central ID

  • PMC3965011

International Standard Serial Number (ISSN)

  • 1362-4962 (Electronic) 0305-1048 (Linking)

Digital Object Identifier (DOI)

  • 10.1093/nar/gkt1144

PubMed ID

  • 24271400
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Additional Document Info

start page

  • D336

end page

  • D346

volume

  • 42

issue

  • Database

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