Ontology highlight
ABSTRACT:
SUBMITTER: Lavery R
PROVIDER: S-EPMC4081102 | biostudies-literature | 2014 Jul
REPOSITORIES: biostudies-literature
Lavery Richard R Maddocks John H JH Pasi Marco M Zakrzewska Krystyna K
Nucleic acids research 20140606 12
We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact ...[more]