Citation for NE-1
German Barcenas
Tom
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Bryan Bishop
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German Barcenas
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Damian Allis
Greetings German and everyone else,
That was about it -
Sims M., Smith B., Helfrich B., Sathaye N., Messick E., Moore
T., Fish R., Rajagopalan M., Rotkiewicz P., Hendricks D.,
Drexler K.E., and Allis D.G. “NanoEngineer-1 – A CAD-based
molecular modeling program for structural DNA nanotechnology.”
Foundations of Nanoscience: Self-Assembled Architectures and
Devices 2008 (FNANO08), Snowbird, UT, USA, April 22-25, 2008,
pgs. 175-178.
We did try to publish an article in the Journal of Computational
Chemistry back in 2008 (prior to FNANO) about the program and
the force field (the reduced-model DNA force field, not the
atomistic one we were working on for diamondoid stuff) to have a
more official citation. The paper was, admittedly, written as
more of a software release announcement than a scientific
article, which meant being very light on the technical details
of the DNA force field - no rigorous testing and comparisons to
fully-atomistic models, just that the capability existed and was
useful for drawing and simulating the larger structural features
of DNA nanostructures (and included representative structures.
And a full description of the reduced-model force field. And the
file exactly as needed to add to GROMACS to run stuff.
Reviewers. Happy to dig up the copy if anyone's interested -
just drop me a sep. line). The attempt to publish on *both* the
GUI and a new force field was, arguably, too much for a single
(not deep enough into the technical weeds) paper.
Worse, the reviewer (honest to goodness) couldn't find the
download button on the website. The last sentence of the paper
was less than helpful to them: "File downloads, up-to-date
information on programs supported within NE1, and version
information about this and subsequent releases are available
from the Nanorex, Inc. website, http://www.nanoengineer-1.com."
We gave up on that specific version of the paper and focused on FNANO-related work. The plan was to try again eventually with both, get more force field testing done, put together more DNA examples for comparison with experiment, etc., but it all (sadly) never got that far.
Thinking small,
Damian
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German Barcenas
Greetings German and everyone else,
That was about it -
Sims M., Smith B., Helfrich B., Sathaye N., Messick E., Moore T., Fish R., Rajagopalan M., Rotkiewicz P., Hendricks D., Drexler K.E., and Allis D.G. “NanoEngineer-1 – A CAD-based molecular modeling program for structural DNA nanotechnology.” Foundations of Nanoscience: Self-Assembled Architectures and Devices 2008 (FNANO08), Snowbird, UT, USA, April 22-25, 2008, pgs. 175-178.
We did try to publish an article in the Journal of Computational Chemistry back in 2008 (prior to FNANO) about the program (and the force fields (both the fully-atomistic and the reduced-model DNA force field) but mostly just the release of the GUI). The paper was, admittedly, written as more of a software release announcement than a scientific article, which meant being very light on the technical details of the DNA force field - no rigorous testing and comparisons to fully-atomistic models, just that the capability existed and was useful for drawing reduced-model versions of DNA nanostructures. Worse still, the DNA Nano functionality was still a work in progress at the time of our submitting the paper and, to the best of my recollection, not yet fully available for unrestricted "download" (as in "Here's the link. Come and get it.").
The review had lots of small critiques of the paper itself (reviewer...), but ended it with:
"I am afraid I can not recommend this paper for publication. However I would like to point out that this is not due to poor quality of the announced software but rather the fact that the software is not yet available, the reduced DNA model is neither published nor explained nor benchmarked and the poor style of the paper."
On 2/10/23 12:06 PM, German Barcenas wrote:
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Damian Allis
That was about it -
Sims M., Smith B., Helfrich B., Sathaye N., Messick E., Moore T., Fish R., Rajagopalan M., Rotkiewicz P., Hendricks D., Drexler K.E., and Allis D.G. “NanoEngineer-1 – A CAD-based molecular modeling program for structural DNA nanotechnology.” Foundations of Nanoscience: Self-Assembled Architectures and Devices 2008 (FNANO08), Snowbird, UT, USA, April 22-25, 2008, pgs. 175-178.
To view this discussion on the web visit https://groups.google.com/d/msgid/nanoengineer-dev/CAFFjVQ5h%2BKFiHijwOTbRov%3DVOXP3ds0yk9xjha2Dge0%2BkCAUnQ%40mail.gmail.com.