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Title: DSSR-Jmol featured in cover image of NAR'17 web-server issue
Post by: xiangjun on June 30, 2017, 08:10:43 pm

The DSSR-Jmol paper, titled "DSSR-enhanced visualization of nucleic acid structures in Jmol" (https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365), has been officially published in the 2017 web-server issue (https://academic.oup.com/nar/issue/45/W1) of Nucleic Acids Research (NAR). Notably, the work has been featured in the cover image (http://forum.x3dna.org/dssr-jmol-integration/cover-image/), as shown below:

(http://jmol.x3dna.org/cover-image/NAR17-web-cover.png)

Quote

Caption: 3D interactive visualization of selected RNA structural features enabled by the DSSR-Jmol integration (http://jmol.x3dna.org (http://jmol.x3dna.org)). Clockwise from upper left: Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red (upper left corner). Structure of the Thermus thermophilus 30S ribosomal subunit in complex with antibiotics (PDB id: 1fjg) in step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5′-end in blue and the 3′-end in red (upper middle). Structure of the classic L-shaped yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram, with the three hairpin loops highlighted in red and the [2,1,5,0] four-way junction loop in blue (upper right corner). Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the horizontal helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions (bottom).

The DSSR-Jmol integration bridges the DSSR command-line analyzing tool and the Jmol molecular viewer seamlessly together via the standard JSON interface. Now users can select DSSR-derived RNA structural features (such as base pairs, double helices, various loops, etc.) and visualize them in novel representations in Jmol interactively. Moreover, fine-grained characteristics of these features can be queried via the Jmol SQL for DSSR. The DSSR-Jmol integration fills a gap in RNA structural bioinformatics, and brings RNA visualization to an entirely new level. The web interface (http://jmol.x3dna.org (http://jmol.x3dna.org)) is fully functional and easy to use, serving a huge user base of researchers, educators, and students alike.

Featured as the cover image of the 2017 NAR web-server issue, DSSR's publicity would surely increase through the DSSR-Jmol integration. Additionally, I've written a new post (on the 3DNA Forum) that provides the scripts and datafiles used to create the cover image (http://forum.x3dna.org/dssr-jmol-integration/cover-image/).

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University