Journal
FRONTIERS IN MOLECULAR BIOSCIENCES
Volume 7, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fmolb.2020.576689
Keywords
MM/CG; molecular mechanics; coarse-grained; hybrid methods; webserver; G protein-coupled receptor; ligand; molecular dynamics simulation
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Funding
- Ernesto Illy Foundation (Trieste, Italy)
- EBRAINS research infrastructure from European Union's Horizon 2020 Framework Programme for Research and Innovation [945539]
- Central Library of Forschungszentrum Julich
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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.
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