With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …

We present parmbsc1, a force field for DNA atomistic simulation, which has been
parameterized from high-level quantum mechanical data and tested for nearly 100 systems …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …

The B-form of DNA can populate two different backbone conformations: BI and BII, defined
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …

We systematically parameterized a coarse-grained (CG) model for DNA that is compatible
with the Martini force field. The model maps each nucleotide into six to seven CG beads and …

Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …

We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-
grained model of DNA similar to that recently introduced in a study of DNA nanotweezers …

We present a method and web server for predicting DNA structural features in a high-
throughput (HT) manner for massive sequence data. This approach provides the framework …