A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations

Citation (APA 7)

Alessandri, R., Thallmair, S., Herrero, C. G., Mera-Adasme, R., Marrink, S. J., & Souza, P. C. (2023). 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 (pp. 1-1). Melville, New York: AIP Publishing LLC.

Abstract

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.