Coarse-Grained DNA Models: Bridging Scales Through Extended Dynamics

M Soñora and LHS Santos and A Alba and A Ballesteros-Casallas and S Pantano, WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 15, e70028 (2025).

DOI: 10.1002/wcms.70028

The cost-effective simulation of biomolecular assemblies using simplified molecular representations has seen significant developments since the beginning of the century. Residue-based coarse-grained (CG) models have become increasingly popular in modeling membranes and protein systems thanks to the speed-up they provide while still offering pseudo-atomistic resolution. However, CG models of DNA have lagged, primarily due to intrinsic complexities such as the dominant role of electrostatics and stacking interactions. This unique challenge has intrigued researchers, leading to significant contributions in the field by the end of the first decade of the century. Here, we provide a comprehensive historical overview of the developments of all-atoms and CG DNA models since the early 1980s. This journey through four decades of DNA modeling aims to highlight the significance of landmark works that shape the development of more complete and accurate simulation tools today.

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