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@article{1816577,
author = {Kuťák, David and Poppleton, Erik and Miao, Haichao and Šulc, Petr and Barišić, Ivan},
article_location = {Basel},
article_number = {1},
doi = {http://dx.doi.org/10.3390/molecules27010063},
keywords = {DNA nanotechnology; file format; molecular file formats; computer-aided design; coarse-grained simulations; DNA origami; DNA-protein engineering; RNA nanotechnology},
language = {eng},
issn = {1420-3049},
journal = {Molecules},
title = {Unified Nanotechnology Format: One Way to Store Them All},
url = {http://dx.doi.org/10.3390/molecules27010063},
volume = {27},
year = {2022}
}
TY - JOUR
ID - 1816577
AU - Kuťák, David - Poppleton, Erik - Miao, Haichao - Šulc, Petr - Barišić, Ivan
PY - 2022
TI - Unified Nanotechnology Format: One Way to Store Them All
JF - Molecules
VL - 27
IS - 1
SP - 1-17
EP - 1-17
PB - MDPI
SN - 14203049
KW - DNA nanotechnology
KW - file format
KW - molecular file formats
KW - computer-aided design
KW - coarse-grained simulations
KW - DNA origami
KW - DNA-protein engineering
KW - RNA nanotechnology
UR - http://dx.doi.org/10.3390/molecules27010063
N2 - The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.
ER -
KUŤÁK, David, Erik POPPLETON, Haichao MIAO, Petr ŠULC and Ivan BARIŠI$\backslash$'C. Unified Nanotechnology Format: One Way to Store Them All. \textit{Molecules}. Basel: MDPI, 2022, vol.~27, No~1, p.~1-17. ISSN~1420-3049. Available from: https://dx.doi.org/10.3390/molecules27010063.
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