Molecular dynamics simulations of DNA–DNA and DNA–protein interactions

Jejoong Yoo, David Winogradoff, Aleksei Aksimentiev

Research output: Contribution to journalReview articlepeer-review


The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA–protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.

Original languageEnglish (US)
Pages (from-to)88-96
Number of pages9
JournalCurrent Opinion in Structural Biology
StatePublished - Oct 2020

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology


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