부산대학교 도서관

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 G\=oMartini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based G\=o-like approach for the study of protein-sugar complexes, and also limitations of this approach are discussed. The G\=oMartini approach was first introduced by Poma et al. J. Chem. Theory Comput. 2017, 13(3), 1366-1374 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 to this approach in the context of the biophysical community.
Comment: 19 pages, 3 figures