The power of coarse graining in biomolecular simulations

被引:435
作者
Ingolfsson, Helgi I.
Lopez, Cesar A.
Uusitalo, Jaakko J.
de Jong, Djurre H.
Gopal, Srinivasa M.
Periole, Xavier
Marrink, Siewert J. [1 ]
机构
[1] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Groningen, Netherlands
关键词
MOLECULAR-DYNAMICS SIMULATIONS; PROTEIN-COUPLED RECEPTORS; RESIDUE FORCE-FIELD; STRUCTURE PREDICTION; STRUCTURAL DETERMINANTS; INTERACTION POTENTIALS; TRANSMEMBRANE HELICES; FOLDING SIMULATIONS; LIPID-BILAYERS; PHASE-BEHAVIOR;
D O I
10.1002/wcms.1169
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
引用
收藏
页码:225 / 248
页数:24
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