GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

Nucleic Acids Res. 2016 Jul 8;44(W1):W455-62. doi: 10.1093/nar/gkw403. Epub 2016 May 10.


GPCR-ModSim ( is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results.

MeSH terms

  • Algorithms
  • Allosteric Regulation
  • Amino Acid Sequence
  • Humans
  • Internet*
  • Ligands
  • Models, Molecular*
  • Molecular Dynamics Simulation
  • Receptor, Angiotensin, Type 2 / chemistry
  • Receptors, G-Protein-Coupled / chemistry*
  • Software*


  • Ligands
  • Receptor, Angiotensin, Type 2
  • Receptors, G-Protein-Coupled