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Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations ... and to analyse the trajectories. ... Here, we present our Martini coarse-grained membrane proteIn dynamics, MERMAID web server, aimed at preparing and running CGMD simulations directly from a publicly available web interface ( Figure 1 ...doi:10.1093/nar/gkz416 pmid:31106328 pmcid:PMC6602572 fatcat:xzxnciqjjnaepifgiyzrgosw3q
The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. ... Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. ... The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ...doi:10.3390/molecules25245934 pmid:33333836 pmcid:PMC7765266 fatcat:wq5ttwweozavba6qhnx7nguzde
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. ... ACKNOWLEDGMENTS We thank Emiliano Ippoliti for the setup of the server and Jonas Goßen for programming advice. ...doi:10.3389/fmolb.2020.576689 pmid:33102525 pmcid:PMC7500467 fatcat:6fwfr6nunvb5fo2tgnvnrq4axm
MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids etc.) for molecular dynamics (MD) simulations at the CG level. ... The MArtini Database (MAD - www.mad.ibcp.fr) is a web server designed for the sharing structures and topologies of molecules parameterized with the Martini coarsegrained (CG) force field. ... Conclusion and perspectives We presented here the MAD server, a new web resource dedicated to the preparation of MD systems with the Martini coarse-grained force field. ...doi:10.1101/2022.08.03.502585 fatcat:zubkw6ftrfdkhdscdlb4zo4v4u
The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing ... such as sirtuins, RAS proteins, or intrinsically disordered proteins. ... The funders had no role in the writing of the manuscript, or in the decision to publish the results. ...doi:10.3390/pr9010071 fatcat:x6pcyzoxevbvhncirfrkqiuppq
Abstracts of the 20th Academic Medical Congress of Piaui, Brazil, COMAPI 2013Abstracts of the 15th International Congress for Medical Students and Young Health Professionals, Romania, Medicalis 2014Abstracts ... We are also grateful to Maria Karpińska for enabling us to work in the Department of Biophysics and Acknowledgement: The study was supported by the grants IGA NT11405-6, GACR 14-37368G, and by the project ... Acknowledgement: We would like to thank all people who helped us during our research work. Special thanks to Beata Modzelewska for her assistance and helpful advice. ...doi:10.5195/ijms.2014.53 fatcat:gmijj74eqfhqlniiiehnptd7dm