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). © The Author(s) 2010.