If you use this server, please cite: Sandal M, Duy TP, Cona M, Zung H, Carloni P, et al. (2013) GOMoDo: A GPCRs Online Modeling and Docking Webserver. PLoS ONE 8(9): e74092. doi:10.1371/journal.pone.0074092
G-protein-coupled receptors (GPCRs) are the largest membrane-bound receptor family expressed by mammalians (encompassing more than 1% of the genome). They are involved in an enormous variety of intra- and extracellular signaling, including detection of light, sense of smell, neurotransmission, inflammation, and cardiac and smooth muscle contractility (Kroeze et al., 2003; Sakmar, 2002). Ligand (or photon) binding to GPCRs activates a cascade of events, producing an electrical signal as output. They are of utmost pharmaceutical relevance, being the targets of almost 30% of all marketed drugs (Landry and Gies, 2008).
This webtool performs automatic homology modeling and ligand docking of GPCR receptors. It uses HHsearch package 1.5.1 for performing sequence alignment. Only GPCR templates are chosen to build 3D model of given sequence by using Modeller 9.10. The obtained 3D model can be verified also with the VADAR server, and then docked with ligands uploaded by users with both Autodock VINA or HADDOCK. Binding pockets can be predicted by the FPOCKET, and structural alignment of models needed for VINA docking is performed by LOVOALIGN
See References for the full list of literature references related to tools used in GOMoDo.
This webtool is built by the Applied Bioinformatics Group at the Department of Biotechnology, University of Verona and by the Institute for Computational Biomedicine (INM-9/IAS-5) of the Forschungszentrum Jülich GmbH and RWTH Aachen University.