标题： 戈马丁尼方法：重新审视接触图的概念和蛋白质复合物的建模 显示英文标题

标题： The GōMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes

摘要： 我们综述了一套基于距离阈值的接触图，用于确定蛋白质和核酸中的天然相互作用。这种接触图大多基于物理和化学构造，但对某些参数（例如距离或原子半径）敏感，并可能忽略一些关键相互作用。此外，我们还评论了一类仅需要几何论证的新接触图。接触图是构建蛋白质及其复合物在Martini 3力场中稳健的GōMartini模型的必要成分。我们介绍了对研究蛋白质-糖复合物的一种流行的基于结构的Gō类似方法的扩展，同时也讨论了该方法的局限性。GōMartini方法最初由Poma等人在Martini 2力场中引入，发表于J. Chem. Theory Comput. 2017, 13(3), 1366-1374，并且最近，在Martini 3力场中用于经历构象变化的蛋白质模拟，该方法已获得黄金标准的地位。我们讨论了几项研究，这些研究在生物物理界背景下支持了这种方法。 显示英文摘要

摘要： 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.