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

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 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).

Figure 1.

The Chimera–Modeller interface. The sequence alignment is displayed in Chimera's Multalign Viewer tool (top). In the dialog for running Modeller (middle left), one of the sequences in the alignment is designated as the target, and at least one structure (associated with another sequence in the alignment) is designated as the template. Structure information is shown to help guide the choice of template. After the run, the resulting models are listed along with various model scores from Modeller in a table (bottom left) and their structures are loaded into Chimera. In this example, the main Chimera window (right) shows the template as an outline and one of the model structures as a ribbon colored by error profile.

Figure 2.

Model of Helicobacter pylori biotin carboxylase based on template 1dv1. TSVMod predicts a C^α RMSD of 3.5 Å. The top ten functional residues predicted by INTREPID are highlighted: seven that are also known from the literature to be involved in catalytic function are colored red, and three representing potential novel predictions are colored blue. These 10 residues are, in descending order of INTREPID importance score: C243 (red), H222 (red), H312 (red), F93 (blue), M304 (red), Y74 (blue), Q226 (blue), Q246 (red), Q250 (red) and Q309 (red). UCSF Chimera was used to load the model from ModBase and produce this figure.

Figure 3.

ModBase Model Details page (e.g. O25458 from the Helicobacter pylori genome data set): Prominently displayed is the model with the highest sequence identity/model length combination. The thumbprints represent all models from the most recent modeling calculation. Models from earlier calculations are also available. A ribbon diagram of the primary model, database annotations, and modeling details are displayed. The pull-down menu provides access to alternative ModBase views and other types of information (if available), such as data about SNPs. The cross-references section contains links to relevant internal and external databases. Through a link to ModWeb (displayed in the inner box), a user can update the model.