GOMoDo: A GPCRs online modeling and docking webserver

PLoS One. 2013 Sep 6;8(9):e74092. doi: 10.1371/journal.pone.0074092. eCollection 2013.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adrenergic Agonists / chemistry*
  • Adrenergic Antagonists / chemistry*
  • Computational Biology
  • Databases, Protein
  • Humans
  • Internet
  • Ligands
  • Molecular Docking Simulation*
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Receptors, Adrenergic, alpha-2 / chemistry*
  • Receptors, Adrenergic, beta-2 / chemistry*
  • Software*

Substances

  • Adrenergic Agonists
  • Adrenergic Antagonists
  • Ligands
  • Receptors, Adrenergic, alpha-2
  • Receptors, Adrenergic, beta-2

Grants and funding

This work has been funded by a grant from the Deutsche Forschungsgemeinschaft (CA 973/6-1) and a grant from Vietnam National Foundation for Science and Technology Development (DFG.2011.01). MS benefited of a postdoctoral fellowship from UniVR. FM is funded by Programma Operativo del Fondo Sociale Europeo 2007/2013 of Friuli Venezia Giulia Region. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.