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

By Mauricio Esguerra, Alexey Siretskiy, Xabier Bello, Jessica Sallander, H. Gutiérrez‐de‐Terán. 2016

66 citations recorded by the source corpus.

GPCR-ModSim (http://open.gpcr-modsim.org) 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.

Subfields: Cellular and Molecular Neuroscience, Molecular Biology

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In Cellular and Molecular Neuroscience

1. Jens Meiler
2. Brian Joseph Bender
3. Brennica Marlow
4. Michael Feig
5. Lim Heo

In Molecular Biology

1. Brian Joseph Bender
2. Brennica Marlow
3. Jens Meiler
4. Lim Heo
5. Michael Feig
6. David Baker

Citations in the corpus

• Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs (2020, methodology): “Servers for the prediction of GPCRs from multiple templates are available including GPCR-ModSim [12], GPCR-I-Tasser [13], GPCRM [14], GPCR-SSFE [15], and GPCRdb [16].”