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Author Topic: Web 3DNA 2.0 is highlighted in NAR web server issue 2019  (Read 468 times)

Offline xiangjun

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Web 3DNA 2.0 is highlighted in NAR web server issue 2019
« on: July 01, 2019, 07:47:39 pm »
It is a great pleasure to see that our article "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" has been highlighted in the cover page of the web server issue of NAR’19. According to the editor, This year, 331 proposals were submitted and 122, or 37%, were approved for manuscript submission. Of those approved, 94, or 77%, were ultimately accepted for publication. Overall, that corresponds to a ~28% acceptance rate.

The cover image and its caption are shown below. Moreover, details on how the cover image was created are available on the 3DNA Forum.

Caption: Examples of customized molecular models that can be generated with 3DNA: (top) a chromatin-like, nucleosome-decorated DNA with the structures of known histone-DNA assemblies placed at user-defined binding sites; (lower left) molecular schematic of a DNA trinucleotide diphosphate illustrating the base planes and reference frames used to construct and analyze 3D nucleic acid-containing structures; (lower right) customized single-stranded tRNA model built from a user-defined base sequence and a set of rigid-body parameters describing the desired placement of successive bases. Color code of base blocks: A, red; C, yellow; G, green; T, blue; U, cyan.
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cllawson

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Re: Web 3DNA 2.0 is highlighted in NAR web server issue 2019
« Reply #1 on: August 07, 2019, 08:03:31 am »
Congratulations Shuxiang, Wilma, and Xiangjun  on your new publication and server, looks great!

Offline xiangjun

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Re: Web 3DNA 2.0 is highlighted in NAR web server issue 2019
« Reply #2 on: August 07, 2019, 09:19:05 am »
Hi Cathy,

Thanks for your kind words about our Web 3DNA 2.0 publication in NAR. Shuxiang has done an excellent job to bring the 3DNA web server up to date and highly usable for the years to come.

I noticed that the cover images of recent issues of the RNA Journal were contributed by the NDB. The cover image and its caption of the August 2019 issue are shown below. Thanks for your generous mention of the 3DNA/blocview program!


"Crystal structure of the metY SAM V riboswitch (Protein Data Bank code: 6fz0; Huang L, Lilley DMJ. Structure and ligand binding of the SAM-V riboswitch. 2018. Nucleic Acids Res 46: 6869–6879). The RNA riboswitch backbone is displayed as a red ribbon; bases are shown as blocks with NDB coloring: A—red, C—yellow, G—green, U—cyan; the intercalating S-adenosylmethionine (SAM) ligand is shown in spacefill with element colors: C—white, N—blue, O—red, S—yellow. The image was generated using 3DNA/blocview and PyMol software. Cover image provided by the Nucleic Acid Database (ndbserver.rutgers.edu)."


Enjoy the summer!

Xiang-Jun
« Last Edit: August 07, 2019, 02:06:24 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cllawson

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Re: Web 3DNA 2.0 is highlighted in NAR web server issue 2019
« Reply #3 on: August 07, 2019, 09:56:08 am »
Thank you Xiang-Jun.

Indeed you may continue seeing such images on RNA Journal, with 3DNA/blocview credited, at least through next year  :)

Offline xiangjun

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Re: Web 3DNA 2.0 is highlighted in NAR web server issue 2019
« Reply #4 on: August 07, 2019, 11:12:19 am »
Hi Cathy,

That's really great -- thanks for sharing the info!

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.