EmDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.

ABSTRACT: Computational modeling of nucleic acids plays an important role in molecular biology, enhancing our general understanding of the relationship between structure and function. Biophysical studies have provided a wealth of information on how double-helical DNA responds to proteins and other molecules in its local environment but far less understanding of the larger scale structural responses found in protein-decorated loops and minicircles. Current computational models of DNA range from detailed all-atom molecular dynamics studies, which produce rich time and spatially dependent depictions of small DNA fragments, to coarse-grained simulations, which sacrifice detailed physical and chemical information to treat larger-scale systems. The treatment of DNA used here, at the base-pair step level w

SUBMITTER: Young RT 

PROVIDER: S-EPMC9177622 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature