Links to external GPCR resourcesGPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs). GPCRdb curates sequence alignments, structures and receptor mutations from literature. Interactive diagrams visualise receptor residues (e.g. snakeplot and helix box plot) and relationships (e.g phylogenetic trees).
GPCRM 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. Two distinct loop modeling techniques are employed - Modeller and Rosetta - and the BCL::Score (membrane-fitted knowledge-based energy function) is used to score the final ranking list of GPCR models.
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 a 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.
GPCR-ModSim 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.
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. It is a community-driven initiative with the final aim to accelerate basic research and beyond the discovery of more efficient and safer therapeutics.
GalaxyWEB The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by ab initio modeling. The method generates reliable core structures from multiple templates and re-builds unreliable loops or termini by using an optimization-based refinement method.
GPCRautomodel attemps to narrow the gap between known structures and receptors of interest to the biologists. Its primary focus is the high-throughput modelization of olfactory receptor proteins and their docking against odorant molecules. The current version of GPCR automodel can potentially be employed to model any GPCR and its interaction with a molecule of interest for the user. The results are displayed in a user friendly web interface.
GOMoDo While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking), we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure.
GPCR-I-TASSER is a computational method designed for 3D structure prediction of G protein-coupled receptors. The target sequence is first threaded through the PDB libary by LOMETS to search for putative templates. If homologous templates are identified, a template-based fragment assembly procedure is used to construct full-length models. Precomputed models can be obtained from GPCR-HGmod.
Mermaid is a web service which helps the users to prepare and run Coarse-grained molecular dynamics simulations (CG-MD) for their computational studies. It provides a simple graphical user interface for the preparation of required input files to perform CG-MD simulations.
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.