title: GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors.
abstract: 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.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden.
authors.forename: Mauricio
authors.initials: M
authors.lastname: Esguerra
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden.
authors.forename: Alexey
authors.initials: A
authors.lastname: Siretskiy
authors.affiliation: Fundación Pública Galega de Medicina Xenómica, Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706, Spain.
authors.forename: Xabier
authors.initials: X
authors.lastname: Bello
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden.
authors.forename: Jessica
authors.initials: J
authors.lastname: Sallander
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden hugo.gutierrez@icm.uu.se.
authors.forename: Hugo
authors.identifier: http://orcid.org/0000-0003-0459-3491
authors.initials: H
authors.lastname: Gutiérrez-de-Terán
mesh_terms: D000465:Algorithms; D000494:Allosteric Regulation; D000595:Amino Acid Sequence; D006801:Humans; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D044139:Receptor, Angiotensin, Type 2 / Q000737:chemistry; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D044139:Receptor, Angiotensin, Type 2; D043562:Receptors, G-Protein-Coupled