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GOMoDo

GPCR structure prediction server

G-protein couple receptors (GPCRs) are a vast superfamily of eukaryotic transmembrane receptors which act as ubiquitously expressed key regulatory elements and constitute more than 30% of current drug targets. Solving GPCR structures is notoriously technically daunting: as of June 2015, structures for only 29 unique GPCRs were available, less than 4% of the GPCR diversity of the human genome (ca. 800 members).

Homology modeling has long been the tool of choice for GPCR structure prediction. However the average sequence identity between members of the superfamily is often below 20%, making target selection and alignment required for homology modeling far from trivial. There is a lack of bioinformatics tools that allow users to go from sequence to docking, as well as letting users guide the procedure with experimental data.

An additional hindrance is that a robust in silico approach to drug design and ligand-receptor investigation requires mastering a wide array of software tools, from alignment to modeling to docking and structural refinement. Experimentally-oriented research groups interested in ligand-GPCR structural information do not necessarily have this breadth of structural bioinformatics expertise; furthermore, even users familiar with modeling and docking software may find a quicker and reproducible method very useful.

Our group, in collaboration with the University of Verona under the supervision of Prof. Dr. Alejandro Giorgetti (INM-9/IAS-5 Associated staff) therefore developed the GPCR Online Modeling and Docking server (GOMoDo). GOMoDo is meant to allow both expert and non-expert users to obtain readily, with minimum effort, biologically and pharmacologically relevant results. GOMoDo puts together state-of-the-art, proven bioinformatic tools in a proven protocol guided by an easy user interface. The procedure herein automated has been already successfully tested multiple times and it is used by us to prepare GPCR models for simulations.

 GPCR structure prediction serverFigure 1. GOMoDo pipeline

The GOMoDo server is temporarily hosted at the University of Verona while it is being moved on the INM-9/IAS-5 own servers. Please reach GOMoDo clicking here.

 

Reference

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


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