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 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.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Graduate Group in Biophysics, University of California at San Francisco, CA 94158, USA, Structural Bioinformatics Unit, Structural Biology and Chemistry department, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France, Université Paris Diderot-Paris 7, école doctorale iViv, Paris Rive Gauche, 5 rue Thomas Mann, 75013 Paris, France, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Webb
authors.forename: Guang Qiang
authors.initials: GQ
authors.lastname: Dong
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.forename: Hao
authors.initials: H
authors.lastname: Fan
authors.forename: Seung Joong
authors.initials: SJ
authors.lastname: Kim
authors.forename: Natalia
authors.initials: N
authors.lastname: Khuri
authors.forename: Yannick G
authors.initials: YG
authors.lastname: Spill
authors.forename: Patrick
authors.initials: P
authors.lastname: Weinkam
authors.forename: Michal
authors.initials: M
authors.lastname: Hammel
authors.forename: John A
authors.initials: JA
authors.lastname: Tainer
authors.forename: Michael
authors.initials: M
authors.lastname: Nilges
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D030562:Databases, Protein; D016333:HIV Protease / Q000737:chemistry; D006801:Humans; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry; D053838:Scattering, Small Angle; D040681:Structural Homology, Protein; D014961:X-Ray Diffraction
chemical_list: D008565:Membrane Proteins; D020543:Proteome; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1