NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.

ABSTRACT: DNA's physical properties play a central role in genome organization and regulation, but simulating its behavior across biologically relevant scales remains a major computational challenge. Coarse grained DNA models have enabled faster simulations, yet they often sacrifice chemical accuracy or produce unphysical conformations, limiting their utility for studying genome structure. A key difficulty has been constructing a model that is both efficient enough for large-scale simulations and faithful to the molecular mechanics of DNA. Here we introduce NEAT-DNA, a new coarse-grained DNA model that resolves longstanding limitations in physical realism and parameter optimization. By combining a physically principled energy formulation with a unified training framework that integrates data from bo

SUBMITTER: Riveros I 

PROVIDER: S-EPMC12637651 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature