The power of coarse graining in biomolecular simulations

Review
Lipid membranes
Proteins
Self-assembly
DNA
Small molecules
Glycans
Author

Helgi I. Ingólfsson, Cesar A. Lopez, Jaakko J. Uusitalo, Djurre H. de Jong, Srinivasa M. Gopal, Xavier Periole, and Siewert J. Marrink

Doi

https://doi.org/10.1002/wcms.1169

Citation (APA 7)

Ingólfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., & Marrink, S. J. (2014). The power of coarse graining in biomolecular simulations. Wiley Interdisciplinary Reviews: Computational Molecular Science, 4(3), 225-248.

Abstract

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.