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MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics

2019 Nucleic Acids Research  
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

CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations

Alessandro Marchetto, Zeineb Si Chaib, Carlo Alberto Rossi, Rui Ribeiro, Sergio Pantano, Giulia Rossetti, Alejandro Giorgetti
2020 Molecules  
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 MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes

Jakob Schneider, Rui Ribeiro, Mercedes Alfonso-Prieto, Paolo Carloni, Alejandro Giorgetti
2020 Frontiers in Molecular Biosciences  
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

Coarse-graining made easy with the MArtini Database Server [article]

Cecile Hilpert, Louis Beranger, Paulo C.T. Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli, Guillaume Launay
2022 bioRxiv   pre-print
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 - 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

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Outi M. H. Salo-Ahen, Ida Alanko, Rajendra Bhadane, Alexandre M. J. J. Bonvin, Rodrigo Vargas Honorato, Shakhawath Hossain, André H. Juffer, Aleksei Kabedev, Maija Lahtela-Kakkonen, Anders Støttrup Larsen, Eveline Lescrinier, Parthiban Marimuthu (+7 others)
2020 Processes  
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

International Journal of Medical Students - Year 2013 - Volume 2 - Supplement

Executive Committee of IJMS
2014 International Journal of Medical Students  
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