GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors
2016 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 44, no W1, W455-W462 p.Article in journal (Refereed) PublishedText
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.
Place, publisher, year, edition, pages
2016. Vol. 44, no W1, W455-W462 p.
IdentifiersURN: urn:nbn:se:uu:diva-301022DOI: 10.1093/nar/gkw403ISI: 000379786800075PubMedID: 27166369OAI: oai:DiVA.org:uu-301022DiVA: diva2:953357
FunderCarl Tryggers foundation , CTS 13:163, CTS KF15:10eSSENCE - An eScience Collaboration
De två första författarna delar förstaförfattarskapet.2016-08-172016-08-172016-08-17Bibliographically approved