Abstract:
Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force field is one of the most widely used CG models for bio-molecular simulations, partly because of the enormous success of its protein model. With the recent release of a new and improved version of the Martini force field - Martini 3 - a new iteration of its protein model was also made available. The Martini 3 protein force field is an evolution of its Martini 2 counterpart, aimed at improving many of the shortcomings that had been previously identified. In this mini-review, we first provide a general overview of the model and then focus on the successful advances made in the short time since its release, many of which would not have been possible before. Furthermore, we discuss reported limitations, potential directions for model improvement and comment on what the likely future development and application avenues are.
摘要:
粗粒度(CG)蛋白质模型已成为研究许多生物蛋白质细节不可或缺的工具。从构象动力学到蛋白质宏观复合物的组织,甚至蛋白质与其他分子的相互作用。Martini力场是生物分子模拟中使用最广泛的CG模型之一,部分原因是其蛋白质模型的巨大成功。随着最近发布的马提尼力场的新版本-马提尼3-其蛋白质模型的新迭代也可用。Martini3蛋白质力场是其Martini2对应物的进化,旨在改善以前发现的许多缺点。在这个小型审查中,我们首先提供模型的总体概述,然后重点介绍自发布以来在短时间内取得的成功进展,其中许多以前是不可能的。此外,我们讨论报告的局限性,模型改进的潜在方向,并评论未来可能的开发和应用途径。