This title appears in the Scientific Report :
2020
Please use the identifier:
http://dx.doi.org/10.3389/fmolb.2020.576689 in citations.
Please use the identifier: http://hdl.handle.net/2128/25811 in citations.
Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes
Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes
Hybrid Molecular Mechanics/Coarse-Grained (MM/CG) simulations help predict ligand poses in human G protein-coupled receptors (hGPCRs), the most important protein superfamily for pharmacological applications. This approach allows the description of the ligand, the binding cavity, and the surrounding...
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Personal Name(s): | Schneider, Jakob |
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Ribeiro, Rui / Alfonso-Prieto, Mercedes / Carloni, Paolo (Corresponding author) / Giorgetti, Alejandro (Corresponding author) | |
Contributing Institute: |
Computational Biomedicine; IAS-5 Jara-Institut Quantum Information; INM-11 Computational Biomedicine; INM-9 |
Published in: | Frontiers in molecular biosciences, 7 (2020) S. 576689 |
Imprint: |
Lausanne
Frontiers
2020
|
DOI: |
10.3389/fmolb.2020.576689 |
Document Type: |
Journal Article |
Research Program: |
Theory, modelling and simulation |
Link: |
Get full text Get full text OpenAccess OpenAccess |
Publikationsportal JuSER |
Please use the identifier: http://hdl.handle.net/2128/25811 in citations.
Hybrid Molecular Mechanics/Coarse-Grained (MM/CG) simulations help predict ligand poses in human G protein-coupled receptors (hGPCRs), the most important protein superfamily for pharmacological applications. This approach allows the description of the ligand, the binding cavity, and the surrounding water molecules at atomistic resolution, while coarse-graining the rest of the receptor. Here, we present the Hybrid MM/CG Webserver (mmcg.grs.kfa-juelich.de) that automatizes and speeds up the MM/CG simulation setup of hGPCR/ligand complexes. Initial structures for such complexes can be easily and efficiently generated with other webservers. The Hybrid MM/CG server also allows for equilibration of the systems, either fully automatically or interactively. The results are visualized online (using both interactive 3D visualizations and analysis plots), helping the user identify possible issues and modify the setup parameters accordingly. Furthermore, the prepared system can be downloaded and the simulation continued locally. |