GOMoDo: A GPCRs online modeling and docking webserver
G-protein coupled receptors (GPCRs) are a superfamily of cell signaling membrane proteins that include >750 members in the human genome alone. They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique...
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| Veröffentlicht in: | PloS one 2013-09, Vol.8 (9), p.e74092-e74092 |
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| creator | Sandal, Massimo Duy, Tran Phuoc Cona, Matteo Zung, Hoang Carloni, Paolo Musiani, Francesco Giorgetti, Alejandro |
| description | G-protein coupled receptors (GPCRs) are a superfamily of cell signaling membrane proteins that include >750 members in the human genome alone. They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking), we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. The GOMoDo server is freely accessible at http://molsim.sci.univr.it/gomodo. |
| doi_str_mv | 10.1371/journal.pone.0074092 |
| format | Article |
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They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking), we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. The GOMoDo server is freely accessible at http://molsim.sci.univr.it/gomodo.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0074092</identifier><identifier>PMID: 24058518</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adrenergic Agonists - chemistry ; Adrenergic Antagonists - chemistry ; Algorithms ; Automation ; Bioinformatics ; Biophysics ; Biotechnology ; Computational Biology ; Computational physics ; Databases, Protein ; Docking ; G protein-coupled receptors ; Genomes ; Genomics ; Homology ; Humans ; Internet ; Laboratories ; Ligands ; Membrane proteins ; Modelling ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Conformation ; Proteins ; Receptors ; Receptors, Adrenergic, alpha-2 - chemistry ; Receptors, Adrenergic, beta-2 - chemistry ; Science ; Servers ; Servers (Computers) ; Signaling ; Software</subject><ispartof>PloS one, 2013-09, Vol.8 (9), p.e74092-e74092</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Sandal et al. 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They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking), we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. 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They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking), we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. 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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Adrenergic Agonists - chemistry Adrenergic Antagonists - chemistry Algorithms Automation Bioinformatics Biophysics Biotechnology Computational Biology Computational physics Databases, Protein Docking G protein-coupled receptors Genomes Genomics Homology Humans Internet Laboratories Ligands Membrane proteins Modelling Molecular Docking Simulation Molecular Dynamics Simulation Protein Conformation Proteins Receptors Receptors, Adrenergic, alpha-2 - chemistry Receptors, Adrenergic, beta-2 - chemistry Science Servers Servers (Computers) Signaling Software |
| title | GOMoDo: A GPCRs online modeling and docking webserver |
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