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About GPCR-SSFE 2.0
The GPCR-Sequence-Structure-Feature-Extractor (SSFE) web server and database provides template suggestions and homology models of Class A GPCRs. GPCR-SSFE 2.0 is based on our published workflow for identifying key sequence and structural motifs in Class A GPCRs which is used to guide template selection and build homology models. The methodology has recently been updated to include 27 template structures, uses a new fingerprint correlation scoring strategy and includes loop modelling.
Users can access the models stored in GPCR-SSFE 2.0 by either browsing the superfamily (subdivided into 10 families) or by searching for results using a UniProt identifier. Users can also enter a GPCR sequence of their choice for analysis by GPCR-SSFE 2.0. Results returned include the suggestion of which template(s) to use for modelling, sequence alignments and homology models of the query GPCR.
About GPCR-SSFE
References
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GPCR-SSFE 2.0 has been updated to include 33 template structures
As of December 2017, five new inactive structures have been added to our pool of templates: CCR2, CCR9, ADORA1, PAR2 and LPAR6. Template selection and modelling has been redone on 1011 GPCR sequences from human, mouse and rat.
Recommended links
Recommended links
Hybrid MM/CG Webserver
Automatic set up of Molecular Mechanics/Coarse-Grained (MM/CG) simulations for human G Protein-Coupled Receptor (GPCR)/ligand complexes.
GPCRdb
Information system for G protein-coupled receptors
GPCRM web service
A web service to predict structures of G-protein-coupled receptors (GPCRs) using advanced homology modeling tools: profile-profile alignment, multiple structural templates, and Z coordinate-based filtering of resulting models.
The online resource for GPCR simulations
GPCRmd is an online platform with web-based visualization capabilities and a comprehensive analysis toolbox that allows scientists from any discipline to visualize, inspect, and analyse GPCR molecular dynamics.
GPCR-ModSim
A pipeline for computational modeling and simulation of G-Protein Coupled Receptors
MDsrv
MDsrv is a web-based tool developed to enhance collaborative research by providing non-experts with easy and quick on-line access to molecular dynamics (MD) simulations. As a member of the nglviewer family, MDsrv channels MD trajectories through a web server using a powerful web application (NGL viewer) to visualize them.
HomolWat (HW)
... is a free tool to incorporate internal water molecules to GPCR structures based on homologous structures with determined water molecules.
NGL viewer
NGL is an on-line viewer for proteins and other molecular structures. It is intended for users of the web application including a graphical interface and for developers who want to use NGL in their own projects.
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Please cite the GPCR-SSFE 2.0 using the following reference:
Worth CL, Kreuchwig F, Tiemann JKS, Kreuchwig A, Ritschel M, Kleinau G, Hildebrand PW and Krause G GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors. Nucleic Acids Res., 2017 Jul 3;45(W1):W408-W415.
Citing GPCR-SSFE
The following reference details the GPCR-SSFE 1.0 web server:
Worth CL, Kreuchwig A, Kleinau G and Krause G (2011) GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models BMC Bioinformatics 12:185.
GPCR-SSFE methodology
The methodology used for template selection by GPCR-SSFE 1.0 is detailed in the following paper:
Worth CL, Kleinau G and Krause G (2009) Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PLoS One 4(9): e7011.
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