Literature DB >> 27477263

Molecular Modelling of G Protein-Coupled Receptors Through the Web.

David Rodríguez1, Xabier Bello1, Hugo Gutiérrez-de-Terán2.   

Abstract

With the recent crystallization of several G Protein-Coupled receptors (GPCRs), homology modelling and all atom molecular dynamics (MD) simulations have proven their usefulness for exploring the structure and function of this superfamily of membrane receptors. Subsequently, automated computational protocols have been implemented as web-based servers in the recent years to produce reliable models of GPCRs, providing partial or global solutions for the structural characterization and molecular simulation of GPCRs. These dedicated modelling services represent an attractive tool for the broader community of public researchers and pharmaceutical companies, in order to assist in the structure-based drug design of GPCRs. We here collect and analyze the existing web servers, among which a previously unreported service, GPCR-ModSim, offers for the first time full atom MD simulations in the pipeline for GPCR molecular modelling.
Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  Database; G Protein-coupled receptor; Molecular dynamics; Structural bioinformatics; Web server

Year:  2012        PMID: 27477263     DOI: 10.1002/minf.201100162

Source DB:  PubMed          Journal:  Mol Inform        ISSN: 1868-1743            Impact factor:   3.353


  10 in total

1.  GOMoDo: A GPCRs online modeling and docking webserver.

Authors:  Massimo Sandal; Tran Phuoc Duy; Matteo Cona; Hoang Zung; Paolo Carloni; Francesco Musiani; Alejandro Giorgetti
Journal:  PLoS One       Date:  2013-09-06       Impact factor: 3.240

Review 2.  GPCRdb: the G protein-coupled receptor database - an introduction.

Authors:  C Munk; V Isberg; S Mordalski; K Harpsøe; K Rataj; A S Hauser; P Kolb; A J Bojarski; G Vriend; D E Gloriam
Journal:  Br J Pharmacol       Date:  2016-06-03       Impact factor: 8.739

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

Authors:  Mauricio Esguerra; Alexey Siretskiy; Xabier Bello; Jessica Sallander; Hugo Gutiérrez-de-Terán
Journal:  Nucleic Acids Res       Date:  2016-05-10       Impact factor: 16.971

4.  Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site.

Authors:  Pierre Matricon; Anirudh Ranganathan; Eugene Warnick; Zhan-Guo Gao; Axel Rudling; Catia Lambertucci; Gabriella Marucci; Aitakin Ezzati; Mariama Jaiteh; Diego Dal Ben; Kenneth A Jacobson; Jens Carlsson
Journal:  Sci Rep       Date:  2017-07-25       Impact factor: 4.379

5.  Mapping the Interface of a GPCR Dimer: A Structural Model of the A2A Adenosine and D2 Dopamine Receptor Heteromer.

Authors:  Dasiel O Borroto-Escuela; David Rodriguez; Wilber Romero-Fernandez; Jon Kapla; Mariama Jaiteh; Anirudh Ranganathan; Tzvetana Lazarova; Kjell Fuxe; Jens Carlsson
Journal:  Front Pharmacol       Date:  2018-08-30       Impact factor: 5.810

6.  The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor.

Authors:  Graham E Jackson; Elumalai Pavadai; Gerd Gäde; Niels H Andersen
Journal:  PeerJ       Date:  2019-08-30       Impact factor: 2.984

7.  Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison.

Authors:  Dorota Latek; Pawel Pasznik; Teresa Carlomagno; Slawomir Filipek
Journal:  PLoS One       Date:  2013-02-28       Impact factor: 3.240

8.  Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure.

Authors:  Margaret M Pruitt; Monica H Lamm; Clark R Coffman
Journal:  BMC Struct Biol       Date:  2013-09-18

9.  GPCRdb: an information system for G protein-coupled receptors.

Authors:  Vignir Isberg; Stefan Mordalski; Christian Munk; Krzysztof Rataj; Kasper Harpsøe; Alexander S Hauser; Bas Vroling; Andrzej J Bojarski; Gert Vriend; David E Gloriam
Journal:  Nucleic Acids Res       Date:  2015-11-17       Impact factor: 16.971

10.  Data for the homology modelling of the red pigment-concentrating hormone receptor (Dappu-RPCHR) of the crustacean Daphnia pulex, and docking of its cognate agonist (Dappu-RPCH).

Authors:  Graham E Jackson; Elumalai Pavadai; Gerd Gäde; Zaheer Timol; Niels H Andersen
Journal:  Data Brief       Date:  2017-10-24
  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.