ModBase, a database of annotated comparative protein structure models and associated resources
| Autor: | Andrej Sali, Ben Webb, Marc A. Marti-Renom, Rachel Karchin, David T. Barkan, Hannah Carter, Libusha Kelly, Fred P. Davis, Parminder Mankoo, David Eramian, Narayanan Eswar, Ursula Pieper |
|---|---|
| Přispěvatelé: | Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Graduate Group in Biophysics, Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Chemistry, The Scripps Research Institute [La Jolla, San Diego]-Skaggs Institute of Chemical Biology, National Institutes of Health [U54 GM094662, U54 GM094625, U54 GM093342, MINOS R01GM105404 to J.A.T. and M.H.], Sandler Family Supporting Foundation (A.S.), Department of Energy Lawrence Berkeley National Lab IDAT program (to J.A.T. and M.H.), European Union [FP7-IDEAS-ERC 294809 to M.N.]. The authors thank Tom Ferrin and the UCSF Resource for Biocomputing, Visualization and Informatics for making UCSF Chimera (supported by [NIGMS P41- GM103311]) available to the ModBase database and tools. Funding for open access charge: NIH., European Project: 294809,EC:FP7:ERC,ERC-2011-ADG_20110310,BAYCELLS(2012), University of California [San Francisco] (UCSF), University of California-University of California, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), The Scripps Research Institute-Skaggs Institute of Chemical Biology, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular MESH: Databases Protein Proteome MESH: Membrane Proteins/chemistry Human immunodeficiency virus (HIV) MESH: Molecular Sequence Annotation Biology MESH: HIV Protease/chemistry computer.software_genre medicine.disease_cause II. Protein sequence and structure motifs and domains 03 medical and health sciences MESH: Protein Structure Tertiary Protein structure HIV Protease X-Ray Diffraction On demand Scattering Small Angle Genetics medicine Humans Databases Protein MESH: Scattering Small Angle 030304 developmental biology MESH: Structural Homology Protein Internet 0303 health sciences MESH: Humans Database 030302 biochemistry & molecular biology Proteolytic enzymes MESH: X-Ray Diffraction Membrane Proteins Molecular Sequence Annotation MODELLER [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] Protein Structure Tertiary MESH: Internet Structural Homology Protein ModBase Protein model computer MESH: Proteome/chemistry MESH: Models Molecular |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, 2013, 42 (D1), pp.D336-D346. ⟨10.1093/nar/gkt1144⟩ Nucleic Acids Research, Oxford University Press, 2013, 42 (D1), pp.D336-D346. ⟨10.1093/nar/gkt1144⟩ |
| ISSN: | 0305-1048 1362-4962 |
| DOI: | 10.1093/nar/gkt1144⟩ |
| Popis: | International audience; ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an auto- mated 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 com- parative 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.prote inmodelportal.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 transmem- brane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|