Delve into the world of nucleic acid simulations, exploring the advancements and applications from 1995 to 2000. This review focuses on the applications and results of molecular dynamics simulations, rather than the methods themselves. The discussion begins with recent advances in simulating nucleic acids in solution, and then provides a detailed summary of the published literature, emphasizing simulations of small nucleic acids in explicit solvent with counterions. By using reliable force fields and modern simulation protocols, this review highlights the observation of A-B transitions in duplex DNA, specific ion binding and hydration, and reliable representation of protein-nucleic acid interactions. Examining major issues and future prospects, the authors offer a valuable resource for researchers in computational biology and related fields. They explore simulations in the absence of explicit solvent, and note the absence of simulations of protein-nucleic acid complexes and modified DNA analogs. This paper examines the future promise for these methods.
Appearing in the Annual Review of Physical Chemistry, this review is relevant to researchers in physical chemistry and related fields. It provides a comprehensive overview of molecular dynamics simulations of nucleic acids, a key area of research in biophysical chemistry.
| Category | Category Repetition |
|---|---|
| Science: Chemistry | 111 |
| Science: Biology (General) | 102 |
| Science: Chemistry: Organic chemistry: Biochemistry | 88 |
| Science: Chemistry: Physical and theoretical chemistry | 70 |
| Science: Physics | 69 |