Chem-Bio Informatics Journal
Online ISSN : 1347-0442
Print ISSN : 1347-6297
ISSN-L : 1347-0442
original
Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures
Yudai YamashitaKotaro WatanabeSatoshi MurataIbuki Kawamata
Author information
JOURNALS FREE ACCESS

2021 Volume 21 Pages 28-38

Details
Abstract

We introduce an automated procedure of coarse-grained molecular dynamic simulation for DNA nanostructure that has great potential for realizing molecular robotics. As DNA origami is now a standardized technology to fabricate DNA nanostructures with high precision, various computer-aided design software has been developed. For example, a design tool called caDNAno with a simple and intuitive interface is widely used for designing DNA origami structures. Further, a simulation tool called oxDNA is used to predict the behavior of such nanostructures based on coarse-grained molecular dynamics. These tools, however, are not linked directly; thus, repeating the cycle of design and simulation is cumbersome to the user. Moreover, the computer skills required to setup, launch, and run an oxDNA simulation are a potential barrier for non-experts. In our proposal, oxDNA simulation can be launched on a web server simply by providing a caDNAno file; the web server then analyzes the simulation results and provides a visual response. The validity of the proposal is demonstrated using an example. The advantages of our proposed method compared with other conventional methods are also described. This simple-to-use interface for user-friendly simulation of DNA origami eliminates stress to users and accelerates the design process of complicated DNA nanostructures such as wireframe architecture.

Information related to the author
International (CC BY 4.0) : The images, videos or other third party material in this article are also included in the article’s Creative Commons license.To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

この記事はクリエイティブ・コモンズ [表示 4.0 国際]ライセンスの下に提供されています。
https://creativecommons.org/licenses/by/4.0/deed.ja
Previous article Next article
feedback
Top