Change search
ReferencesLink to record
Permanent link

Direct link
GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Hosp Clin Univ Santiago, Fdn Publ Galega Med Xenom, Santiago De Compostela 15706, Spain..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
Show others and affiliations
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
Abstract [en]

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.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-301022DOI: 10.1093/nar/gkw403ISI: 000379786800075PubMedID: 27166369OAI: oai:DiVA.org:uu-301022DiVA: diva2:953357
Funder
Carl Tryggers foundation , CTS 13:163, CTS KF15:10eSSENCE - An eScience Collaboration
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2016-08-17 Created: 2016-08-17 Last updated: 2016-08-17Bibliographically approved

Open Access in DiVA

fulltext(2911 kB)24 downloads
File information
File name FULLTEXT01.pdfFile size 2911 kBChecksum SHA-512
eaa75b32cb88a76d84e3551e4e4eb4325f24f648a0c3debe38726872c672c630a6ca8b96e584a02b7502fa1ca40c0f98450bb3930d759cfd59b441275244b02e
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Esguerra, MauricioSiretskiy, AlexeySallander, JessicaGutierrez-de-Teran, Hugo
By organisation
Computational Biology and BioinformaticsDepartment of Cell and Molecular Biology
In the same journal
Nucleic Acids Research
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 24 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 55 hits
ReferencesLink to record
Permanent link

Direct link