GOMoDo: A GPCRs Online Modeling and Docking Webserver
By Massimo Sandal, Tran Phuoc Duy, M.S. Cona, H. Zung, Paolo Carloni, Francesco Musiani, Alejandro Giorgetti. 2013
80 citations recorded by the source corpus.
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 M odeling and D ocking), 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.
Subfields: Cellular and Molecular Neuroscience, Molecular Biology, Spectroscopy
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In Cellular and Molecular Neuroscience
In Molecular Biology
- Gerd Krause
- Slawomir Filipek
- Agnieszka Sztyler
- Catherine L. Worth
- Annika Kreuchwig
- Gunnar Kleinau
- Dorota Latek
- Przemyslaw Miszta
Citations in the corpus
- GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors (2016, methodology): “Consequently, several dedicated protocols for modeling GPCRs have been developed, the following being implemented in web servers: GPCRM (5), GPCR-SSFE (6), GOMoDo (7) and GPCR-ModSim (8) all performing homology-based modeling, while GPCR-I-TASSER (9) uses the threading paradigm.”
- GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models (2018, background): “The GOMoDo (GPCR Online MOdeling and DOcking server) performs automatic homology modeling using Modeller and then ligand docking using AutoDock VINA or HADDOCK when experimental information on ligand binding site is available.”
- GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors (2017, methodology): “However, when loops are included in the RMSD calculations for the ETB receptor, GPCR-I-TASSER and GoMoDo scored better (Table 1).”
- GPCRdb: an information system for G protein-coupled receptors (2015, unknown): “Furthermore, GPCRdb contains links to several specialized GPCR servers for homology modelling: GPCRM (38), GoMoDo (39) and SSFE (40); and molecular dynamics: GPCR Mod-Sim (41).”