Institute of Fundamental Technological Research

We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g., distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust Gō-Martini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based Gō--like approach to the study of protein–sugar complexes, and the limitations of this approach are also discussed. The Gō-Martini approach was first introduced by Poma et al. (J. Chem. Theory Comput. 13, 1366 (2017)) in Martini 2 force field, and recently, it has gained the status of gold standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support for this approach in the context of the biophysical community.

Martini 3,Structure-based coarse-graining,SMFS,biomolecules,GoMartini

coarse-grained method, machine learning, multiscale approach, biopolymers, aggregation, GōMartini approach, Martini 3, nanomechanics