Coarse-Grained Protein Models and Their Applications

被引：716

作者：

Kmiecik, Sebastian ^{[1
]}

Gront, Dominik ^{[1
]}

Kolinski, Michal ^{[2
]}

Wieteska, Lukasz ^{[1
,3
]}

Dawid, Aleksandra Elzbieta ^{[1
]}

Kolinski, Andrzej ^{[1
]}

机构：

[1] Univ Warsaw, Fac Chem, Pasteura 1, PL-02093 Warsaw, Poland

[2] Polish Acad Sci, Bioinformat Lab, Mossakowski Med Res Ctr, Pawinskiego 5, PL-02106 Warsaw, Poland

[3] Med Univ Lodz, Dept Med Biochem, Mazowiecka 6-8, PL-92215 Lodz, Poland

来源：

CHEMICAL REVIEWS | 2016年 / 116卷 / 14期

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; MONTE-CARLO SIMULATIONS; INTRINSICALLY DISORDERED PROTEINS; DEAD-END ELIMINATION; ATOMIC-LEVEL CHARACTERIZATION; PREDICTIVE ENERGY LANDSCAPES; ENHANCED SAMPLING TECHNIQUES; KNOWLEDGE-BASED POTENTIALS; NOVO STRUCTURE PREDICTION; UNRES FORCE-FIELD;

D O I：

10.1021/acs.chemrev.6b00163

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation time scales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems. In this review we provide an overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions. A more detailed description is given for applications of coarse-grained models suitable for efficient combinations with all-atom simulations in multiscale modeling strategies.

引用

页码：7898 / 7936

页数：39

共 621 条

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