The power of coarse graining in biomolecular simulations

By Helgi I. Ingólfsson, Cesar A. López, J. Uusitalo, D. D. de Jong, Srinivasa Murthy Gopal, Xavier Periole, Siewert-Jan Marrink. Wiley Interdisciplinary Reviews. Computational Molecular Science, 2013

542 citations recorded by the source corpus.

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.

Subfields: Ecology, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/182643aecf824e5c511c617a825d7e39cccbd1bc

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. ST John
2. Siewert-Jan Marrink
3. Gábor Csányi
4. Alexander V. Shapeev
5. Evgeny V. Podryabinkin
6. K. Müller
7. Alexandre Tkatchenko
8. James R. Kermode

In Molecular Biology

1. Helgi I. Ingólfsson
2. Svetlana Baoukina
3. Djurre H. De Jong
4. Siewert-Jan Marrink
5. ST John
6. Gábor Csányi

Citations in the corpus

• Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. (2016, methodology): “Moreover, they tend to be comparatively transferable between state points [17].”
• Martini straight: Boosting performance using a shorter cutoff and GPUs (2016, methodology): “Several methods to increase the sampling are available, among which the use of designated hardware [2], distributed sampling [3], enhanced sampling methods [4] and the use of coarse grain (CG) models [5].”