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A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations
In: A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules, chap. 1, AIP Publishing LLC. (ISBN: 978-0-7354-2524-8).
Martini 3 is the new version of a widely used coarse-grained (CG) model that have been extensively parameterized to reproduce experimental and thermodynamic data. Based on a building-block approach, the new version shows a better coverage of the chemical space and more accurate predictions of interactions and molecular packing in general. Given these improvements, the Martini 3 model allows new applications such as studies involving protein–ligand interactions. In this chapter, a summary of the key elements of the new Martini version is presented, followed by an example of a practical application: a simulation of caffeine binding to the buried pocket of the adenosine A2A receptor, which is part of the GPCR family. Formulated as a hands-on tutorial, this chapter contains guidelines to build CG models of important systems, such as small drug-like molecules, transmembrane proteins, and lipid membranes. Finally, the last sections contain an outlook of possible future developments and notes describing useful information, limitations, and tips about Martini.
Martini force field, coarse graining, molecular dynamics
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