Advances in coarse-grained modeling of macromolecular complexes

Abstract

Recent progress in coarse-grained (CG) molecular modeling and simulation has facilitated an influx of computational studies on biological macromolecules and their complexes. Given the large separation of length- and time-scales that dictate macromolecular biophysics, CG modeling and simulation are well-suited to bridge the microscopic and mesoscopic or macroscopic details observed from all-atom molecular simulations and experiments, respectively. In this review, we first summarize recent innovations in the development of CG models, which broadly include structure-based, knowledge-based, and dynamics-based approaches. We then discuss recent applications of different classes of CG models to explore various macromolecular complexes. Finally, we conclude with an outlook for the future in this ever-growing field of biomolecular modeling.

Correction of coarse-graining errors by a two-level method: Application to the Asakura-Oosawa model

“…This is of the required form (2). The distribution P b has a characteristic form at the critical point.…”

“…1(a). A great deal of effort 1,2,8,9,13,14 has gone into developing energy functions E c such that coarse averages such as A c provide good estimates of the corresponding fine average A f . This obviously requires that p c ≈ p m .…”

“…[3][4][5] Alternatively, one may develop a coarse-grained (CG) model that captures quantitatively the behaviour of a more detailed (fine-grained, FG) model. 2,[6][7][8][9] This second type of application is one of the foundations of multi-scale modelling approaches. 10,11 Enormous theoretical and computational effort has been invested in the development of accurate CG models.…”

Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

“…All‐atom molecular dynamics (MD) simulation of large biomolecules can be prohibitively expensive. To solve this problem, many researchers have devoted to developing the so‐called coarse‐grained (CG) models for accelerating simulation. The CG models could be constructed from the fine‐grained models such as all‐atom model by using the “bottom‐up” strategies .…”

Minimal coarse-grained models for molecular self-organisation in biology

“…These models originate in statistical mechanics and soft matter physics where they have been traditionally used to describe collective behaviour of polymers, nanoparticles, and colloids [4]. Unlike bottom-up coarse-grained models, which use a prescribed coarse-graining procedure to retain statistical accuracy or to preserve substantial information about sub-molecular details [5,6], the minimal coarsegrained models we describe here are at heart top-down. Instead of focusing on molecular details, they typically try to capture collective phenomena and the generality of the process under study.…”