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Protocols

GPCR-ModSim specifications

Information


Unique identifier OMICS_14468
Name GPCR-ModSim
Alternative name G-protein coupled receptors Modeling Simulation
Interface Web user interface
Restrictions to use None
Input data GPCR-ModSim offers two possible ways to enter a GPCR sequence: copy and paste a sequence, or enter a a Uniprot ID directly in the sequence box.
Input format FASTA
Output data After submitting the target sequence, the first output provided is the MSA of the target sequence with the selected group of templates. GPCR-ModSim also provides a report with detailed information of the sequence identities between the target sequence and each template, divided by topological regions.
Output format FASTA, PDF
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Hugo Gutierrez-de-Teran

Publications for G-protein coupled receptors Modeling Simulation

GPCR-ModSim citations

 (8)
library_books

GPCRdb in 2018: adding GPCR structure models and ligands

2017
Nucleic Acids Res
PMCID: 5753179
PMID: 29155946
DOI: 10.1093/nar/gkx1109

[…] orms the best, especially in the overall and 7TM. In contrast, three modeling web servers (gray background) perform best in different categories; SWISS-MODEL: overall, GPCRM: 7TM and ligand site, and GPCR-ModSim: ECL2. As could be expected, the RMSDs of the overall and 7TM models correlate directly with the sequence similarities and identities to the main template (bottom of figure). Altogether, t […]

library_books

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)

2017
PMCID: 5683752
PMID: 29159233
DOI: 10.1016/j.dib.2017.10.045

[…] ders . The class of GPCR and trans-membrane (TM) helix predictions were computed on-line using (http://www.imtech.res.in/raghava/gpcrpred/) and (http://bioinf.cs.ucl.ac.uk/psipred/) respectively.The GPCR-ModSim Web server (http://gpcr-modsim.org/) was used for template selection and preliminary sequence alignment. Modeler 9v7 was used to construct 3D models of the receptor. The quality of the c […]

library_books

Rosetta Broker for membrane protein structure prediction: concentrative nucleoside transporter 3 and corticotropin releasing factor receptor 1 test cases

2017
BMC Struct Biol
PMCID: 5543540
PMID: 28774292
DOI: 10.1186/s12900-017-0078-8

[…] eins such as I-TASSER [] or FILM3 [] and a large number of homology-based methods often dedicated to only one protein family, e.g., G protein-coupled receptors (GPCR-I-TASSER [], GPCRM [], GOMoDo [], GPCR-ModSim []) [].The accuracy of the generated hCNT3 model in its N-terminal part could be assessed, e.g., by scoring it against empirical data such as cross-linking data []. Unfortunately, no such […]

call_split

Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A2A adenosine receptor binding site

2017
Sci Rep
PMCID: 5526870
PMID: 28743961
DOI: 10.1038/s41598-017-04905-0
call_split See protocol

[…] sphatidylcholine (POPC) membrane bilayer was first equilibrated around the A2AAR structure with periodic boundary conditions using the 4.5.5 version of GROMACS. These simulations were setup using the GPCR-ModSim protocol and the OPLS all atom (OPLSAA) force field, TIP3P waters, and Berger lipid parameters. All protein atoms were tightly restrained to their initial coordinates and the hydrated memb […]

library_books

Experiences with workflows for automating data intensive bioinformatics

2015
Biol Direct
PMCID: 4539931
PMID: 26282399
DOI: 10.1186/s13062-015-0071-8

[…] difficult for us to use graphical platforms such as Galaxy. Recently, however, we have deployed a private cloud where we aim to provision images containing workflow systems like Galaxy, Chipster, and GPCR-ModSim [], which we believe will enable us to reach a larger scientific community. We are experimenting with the workflow system Luigi on our HPC system, and CloudGene [] on a previously establis […]

call_split

Structural and Energetic Effects of A2A Adenosine Receptor Mutations on Agonist and Antagonist Binding

2014
PLoS One
PMCID: 4186821
PMID: 25285959
DOI: 10.1371/journal.pone.0108492
call_split See protocol

[…] The two starting structures were treated with the membrane insertion and equilibration protocol implemented in the GPCR-ModSim web-server . Briefly, the system is embedded in a pre-equilibrated POPC (1- palmitoyl-2-oleoyl phosphatidylcholine) membrane model so that the TM bundle is parallel to the vertical axis of […]

Citations

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GPCR-ModSim institution(s)
Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden; Fundacion Publica Galega de Medicina Xenomica, Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
GPCR-ModSim funding source(s)
Carl Trygger Fundation [CTS 13:163, CTS KF15: 10]; Swedish strategic research programme eSSENCE

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