作者
Luís Borges-Araújo, Ilias Patmanidis, Akhil P Singh, Lucianna HS Santos, Adam K Sieradzan, Stefano Vanni, Cezary Czaplewski, Sergio Pantano, Wataru Shinoda, Luca Monticelli, Adam Liwo, Siewert J Marrink, Paulo CT Souza
发表日期
2023/10/3
来源
Journal of Chemical Theory and Computation
卷号
19
期号
20
页码范围
7112-7135
出版商
American Chemical Society
简介
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical …
引用总数
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