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

Nucleic acids research | Jan 23, 2011

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 RIS Download

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

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Associated grants

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

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PhyloFacts

It contains pre-calculated structural and phylogenomic analyses of over 57,000 protein families and domains. The PhyloFacts resource includes "books" for protein families across the Tree of Life. Each book includes a multiple sequence alignment, one or more phylogenetic trees, predicted subfamilies, predicted 3D protein structures, active sites and other key residues, cellular localization, and Gene Ontology (GO) annotations and evidence codes. PhyloFacts includes hidden Markov models for classification of user-submitted (DNA or protein) sequences to protein families and subfamilies across the tree of life. Our primary current focus is on covering all the gene families represented in the human genome and all structural domains, but plan to expand the resource to include all proteins in all species. The protein families in this resource typically contain homologs from many species. The phylogenetic distribution of a protein family can vary from highly restricted (e.g., to hominidae or mammals) to throughout the tree of life. Gathering homologs from many divergent species enables us to take advantage of experimental investigations in different systems, and allows powerful inferences of function and structure that might not otherwise be possible.

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