title: 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).
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158, USA.
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Webb
authors.forename: David T
authors.initials: DT
authors.lastname: Barkan
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.forename: Avner
authors.initials: A
authors.lastname: Schlessinger
authors.forename: Hannes
authors.initials: H
authors.lastname: Braberg
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yang
authors.forename: Elaine C
authors.initials: EC
authors.lastname: Meng
authors.forename: Eric F
authors.initials: EF
authors.lastname: Pettersen
authors.forename: Conrad C
authors.initials: CC
authors.lastname: Huang
authors.forename: Ruchira S
authors.initials: RS
authors.lastname: Datta
authors.forename: Parthasarathy
authors.initials: P
authors.lastname: Sampathkumar
authors.forename: Mallur S
authors.initials: MS
authors.lastname: Madhusudhan
authors.forename: Kimmen
authors.initials: K
authors.lastname: Sjölander
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ferrin
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Burley
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D003196:Computer Graphics; D030562:Databases, Protein; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D053838:Scattering, Small Angle; D016415:Sequence Alignment; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface; D014961:X-Ray Diffraction
chemical_list: D001426:Bacterial Proteins; D010455:Peptides; D011506:Proteins