3DNA is a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid-containing structures. The software is applicable not only to DNA (as the name 3DNA may imply) but also to complicated RNA structures and DNA-protein complexes. In 3DNA, structural analysis and model rebuilding are two sides of the same coin: the description of the structure is rigorous and reversible, thus allowing for its exact reconstruction based on the derived parameters.
![](/uploads/1/2/7/6/127614135/582943999.jpg)
3DNA automatically detects all non-canonical base pairs, base triplets and higher-order associations (collectively termed multiplets), and coaxially stacked helices; provides a comprehensive collection of fiber models of regular DNA and RNA helices; generates highly effective schematic presentations that reveal key features of nucleic-acid structures; performs undisturbed, and have facilities for the analysis of molecular dynamics simulation trajectories.is. It is a representative of what would become the brand new version 3 of 3DNA.
Free download 3DNA Desktop 1.1 for Windows 10. 3DNA is a 3D desktop enhancer that improves the way you work with Windows and the Web. You can choose from different 3D Add-on Worlds to explore and customize with 100's of themes and skies for an immersive and entertaining desktop. 3DNA works by overlayi. I think it was called 3dna desktop. Original Poster2. CERN unveils list of Microsoft ALTernative software: the MALT Project.
DSSR consolidates, refines, and significantly extends the functionality of 3DNA v2.x for RNA structural analysis. The Kribelbauer et al. Article, has recently been published in the Journal of Molecular Biology ( JMB). I am honored to be among the author list, and I learned a lot during the process. For the project, I added the -methyl-C (short-form: -5mc) option to SNAP (v1.0.6-2019sep30) for the automatic identification and annotation of DNA-transcription factor (TF) complexes containing 5-methyl-cytosine (5mC). The results are presented in a dynamic table, easily accessible at URL, and summarized in Fig.
1 “Structural basis of how TFs recognize methylated DNA” (see below) of the JMB paper.Details on the SNAP-enabled curation of TF- DNA complexes containing 5mC from atomic coordinates in the Protein Data Bank ( PDB) are available in a tutorial page at. In essence, the process can be easily understood via a concrete example with, as shown below. X3dna-snap -methyl-C -type=base -i=4m9e.pdb -o=4m9e-5mC.outHere the -methyl-C option is specific for 5mC- DNA, and -type=base ensures that at least one DNA base atom is contacting protein amino acid(s). If these conditions are fulfilled, SNAP would produce two additional 5mC-related files, apart from the normal output file (i.e., as specified in the example):. — a simple text file with the following contents:4m9e:B.5CM5: stacking-with-A.ARG443 is-WC-paired is-in-duplex +:GcG/cGC4m9e:C.5CM5: other-contacts is-WC-paired is-in-duplex -:cGT/AcG.
— a corresponding PDB file, potentially multi-model, two as in this case. Moreover, the cluster of interacting residues ( DNA nucleotides and protein amino acids) is oriented in the standard base reference frame of 5mC, allowing for easy comparison and direct overlap of multiple clusters.In practice, SNAP needs to take care of many details for the automatic identification and annotation of 5mC- DNA-TF complexes directly from PDB entries. For example, 5mC in DNA is designated 5CM and the 5-methyl carbon atom is named C5A in the PDB (see the blogpost ).
Moreover, the -type=base option is employed to ensure that base atoms (regardless sugar-phosphate atoms) of 5mC are directly involved in interactions with amino acids.It is also worth noting the combined use of DSSR for the generation of molecular images (rendered with PyMOL), as shown below. Here the DSSR options -block-file=fill-hbond ( fill to fill base rings and hbond to draw hydrogen bonds) and -cartoon-block=sticks-label are used. The 3DNA DSSR/SNAP combo is a unique and powerful toolset for structural bioinformatics, as demonstrated in (see my blogpost ). The JMB paper represents yet another example. I can only expect to see more combined DSSR/SNAP applications in the future. A couple of months ago, I came across the on G-quadruplexes (G4s). I checked the “Online tools” section and found a few links to G4 databases and sequence-based predication programs (e.g., G4Hunter).
No tools, however, were listed for G4 identification and characterization from 3D atomic coordinates as those deposited in the Protein Data Bank ( PDB). So I filled out the contact form and provided a brief description of 3DNA- DSSR, including a link to the website of.I’ve recently visited the G4-society website again. I am pleased to see that 3DNA- DSSR is now listed under as a “program for detections/annotations of G4 from atomic coordinates in PDB or PDBx/mmCIF format”. The G4 module of 3DNA- DSSR has been created to streamline the identification and annotation of 3D structures of G4s. The collection of G4s in the PDB, available at, is updated weekly. It represents a unique resource for the G4 community.
Hopefully, its value will be more widely appreciated thanks to the link from the G4-society website.At the, I noticed the following two items in the “News” section (on December 13, 2019): The Quadruplex Meeting Reportwritten by Jean-Louis Mergny. Reading through the report, I noticed the following:Jonathan B. Louisville, KY, USA) provided an overview and historical perspective of the quadruplex field in his inaugural lecture. As of August 2019, the quadruplex field gathers 8467 articles and 253,174 citations in the Science Citation Index.
Over 200 G4 structures are available in the PDB.I did not know how the survey of G4s in the PDB was performed. Based on my data, the PDB-G4 structures was already over 300 as of August 2019. As of December 11, 2019, the number of is 329. Importantly, the PDB-G4 website compiled using 3DNA- DSSR contains not only citation information but also detailed annotations and schematic images not available elsewhere. Here are a few recent examples:. — “Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3’ terminus.” by Andralojc et al. In RNA (2019).
— “Two-quartet kit. G-quadruplex is formed via double-stranded pre-folded structure.” by Kotar et al.
In Nucleic Acids Res. (2019). — “Structure and functional reselection of the Mango- III fluorogenic RNA aptamer.” by Trachman et al. (2019). —“Structure of a (3+1) hybrid G-quadruplex in the PARP1 promoter.” by Sengar et al. In Nucleic Acids Res. (2019).The Important Paperby Emilia Puig Lombardi and Arturo Londoňo-Vallejo in Nucleic Acids Res.
(2019), which presents an updated overview of G4 prediction algorithms. I am impressed by the large number of sequence-based G4 prediction software tools, including the most recent. Nevertheless, as noted by the authors in the concluding remarks, “All computational G-quadruplex prediction approaches have their drawbacks and limitations despite the recent advances in the field and the introduction of validation steps based on experimental data.”The G4 module in 3DNA- DSSR belongs to a completely different category of software tool. It does not ‘predict’ G4 propensity/stability from a base sequence, but identify and annotate G4s in a 3D atomic coordinate file. It complements sequence-based predicting tools by gaining insights into the 3D G4 structures and refining folding rules to improve performance of prediction tools. Based on my knowledge, the 3D G4 structures contains features that are not captured by any of the sequence-based prediction tools.While reading the review article, I found Fig. 1 informative (see below).
The right side of Fig. 1A shows a “cartoon representation of the Oxytricha telomeric DNA G4 crystal structure ( PDB accession 1JPQ (112))” using PyMOL.
In comparison, the cartoon-block image auto-generated via 3DNA- DSSR and PyMOL for is shown at the bottom. The DSSR-PyMOL version is obviously different, presumably simpler and more informative, from that illustrated in Fig. I recently performed a quick survey of the cover images of the RNA journal in 2019. I was pleased to find that 9 out of the 12 cover images were provided by the where 3DNA/blockview and PyMOL were employed, as noted below:The RNA backbone is displayed as a red ribbon; bases are shown as blocks with NDB coloring: A—red, C—yellow, G—green, U—cyan; geneticin ligands are shown in spacefill with element colors: C—white, N—blue, O—red. The image was generated using 3DNA/blocview and PyMol software.Details of the 9 cover images are listed below:. Rhodobacter sphaeroides Argonaute with guide RNA/target DNA duplex containing noncanonical A-G pair ( PDB code: 6d9k).
Group I self-splicing intron P4-P6 domain mutant U131A ( PDB code: 6d8l). Crystal structure of T. Thermophilus 50S ribosomal protein L1 in complex with helices H76, H77, and H78 of 23S RNA ( PDB code: 5npm). Crystal structure of ykoY-mntP riboswitch chimera bound to cadmium ( PDB code: 6cc3).
G96A mutant of the PRPP riboswitch from T. Mathranii bound to ppGpp ( PDB code: 6ck4).
Crystal structure of the metY SAM V riboswitch ( PDB code: 6fz0). Crystal structure of protease factor Xa bound to RNA aptamer 11F7t and rivaroxaban ( PDB code: 5vof). Drosophila melanogaster nucleosome remodeling complex ( PDB code: 6f4g). Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with Geneticin ( PDB code: 5xz1)Here is the composite figure of the 9 cover images.See also:. I’ve created a web API to 3DNA programs, which currently includes x3dna-dssr, x3dna-snap, and x3dna-fiber.
![Programs Like 3dna Desktop Programs Like 3dna Desktop](http://3.bp.blogspot.com/-_CQ8KiVOg6w/Uk2Aqy-JWqI/AAAAAAAABIU/NTQAil5b6KA/s1600/336.jpg)
The overall help message is available via. Individually, each program is accessed as below. Help message on x3dna-dssr ( DSSR): Usage with 'http' (HTTPie):http -f options url= model@http - display this help messageOptions:json=true-or-FALSE(default) e.g., json=true # JSON outputpair=true-or-FALSE(default) e.g., pair=1 # base-pair onlyhbond=true-or-FALSE(default) e.g., hbond=t # H-bonding infomore=true-or-FALSE(default) e.g., more=y # further detailsRequired parameter:url=URL-to-coordinate-file e.g., url=e.g., [email protected]# Only one must be specified.
'url' precedes 'model' when both are specified.# The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped.Examples:http -f url=-f [email protected] pair=1# with 'curl'curl -F 'url=-F '[email protected]' -F 'pair=1'Note:The web API has an upper limit on coordinate file size (gzipped). The website (see screenshot below) aims to showcase DSSR-enabled cartoon-block schematics of nucleic acid structures using PyMOL. It presents a simple interface to browse pre-calculated PDB entries with a set of default settings: long rectangular blocks for Watson-Crick base-pairs, square blocks for G-tetrads in G-quadruplexes, with minor-groove edges in black.
Users can also specify an URL to a PDB- or mmCIF-formatted file or upload such an atomic coordinates file directly, and set several common options to customerize to the rendered image.Moreover, a web API to DSSR-PyMOL schematics is available to allow for its easy integration into third-party tools.Input a PDB idPre-calculated cartoon-block images together with summary information are available for PDB entries of nucleic-acid-containing structures. Note that gigantic structures like ribosomes that are only represented in mmCIF format are excluded from the resource. The base block images are most effective for small to medium-sized structures.Here are a few examples:., the crystal structure of yeast phenylalanine tRNA at 1.93-Å resolution., the major conformation of the internal loop 5’ GAGU/3’ UGAG. ”, the crystal structure of an RNA quadruplex containing inosine-tetrad., the crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41., crystal structure of the Oct-1 POU domain bound to an octamer site., the crystal structure of an E.
Coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ionsEach entry is shown with images in six orthogonal perspectives: front, back, right, left, top, bottom. The ‘front’ image (upper-left in the panel) is oriented into the most-extended view with the DSSR -blocview option. The corresponding PyMOL session file and PDB coordinate file are available for download. One can also visualize the structure interactively via. Sample PDB entriesUsers can browse random samples of pre-calculated PDB entries.
The number should be between 3 and 99, with a default of 12 entries (see below for an example). Simply click the ‘Submit’ button or the “Random samples (3 to 99)”: link to see results of randomly picked 12 PDB entries each time. Specify a coordinate fileThe atomic coordinate file must be in PDB or mmCIF format, and can be optionally gzipped (.gz). One can either specify an URL to or select a coordinate file.
Several common options are available to allow for user customizations. Web API help message Usage with 'http' (HTTPie):http -f options url= model@http - for a pre-calculated PDB entryhttp - display this help messageOptions:blockfile=styles-in-free-text-format e.g., blockfile=wc-minorblockcolor=nt-selection-and-color e.g., blockcolor='A:pink'blockdepth=thickness-of-base-block e.g., blockdepth=1.2r3dfile=true-or-FALSE(default) e.g., r3dfile=truerawxyz=true-or-FALSE(default) e.g., rawxyz=trueRequired parameterurl=URL-to-coordinate-file e.g., url=e.g., [email protected]# Only one must be specified. 'url' precedes 'model' when both are specified.# The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped.Exampleshttp -f blockfile='wc-minor' [email protected] r3dfile=thttp -f url=-d -o 1ehz.pnghttp -d -o 1ehz.png# with 'curl'curl -F '[email protected]' -F 'blockfile=wc-minor' -F 'r3dfile=1'curl -F 'url=-o 1ehz.pngcurl -o 1ehz.pngSample images. While reading, I noticed SNAP and DSSR being mentioned. The detailed citations are as below:Information about individual nucleotide–residue interactions is also provided, such as hydrogen bonding, interaction geometry (based on SNAP (10)), buried solvent accessible surface areas and identification of the interacting residue and nucleotide moieties DNAproDB assigns a geometry for every nucleotide–residue interaction identified using SNAP, a component of the 3DNA program suite (10). The residues for which probabilities are shown are those with planar side chains so that a stacking conformation can be defined.Base pairing and base stacking between nucleotides are identified using the program DSSR (20).and are two (relatively) new programs in the 3DNA software suite.
As the author, I am always glad to see them being cited explicitly in literature. The fact that SNAP and DSSR are cited together by, however, is especially significant.
I am aware of the, but I definitely like the updated one better. This is what I recently wrote in:Regarding DNA-protein interactions in general, you may want to have a look of DNAproDB from the Remo Rohs laboratory.
A new paper has just been published in NAR, ‘DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes’.I’ve no doubt that SNAP and DSSR would be widely used in applications related to DNA/RNA structural bioinformatics. DSSR (to a lesser extent, SNAP) represents my view of what a scientific software tool should be. Recently I read the article in Bioinformatics by Popenda et al. In this work, the authors proposed an ONZ classification scheme of G-tetrads in intramolecular G-quadruplexes (G4) as shown below ( Fig. 2 in the publication):I am glad to find that DSSR has been used as a component in their computational tool to automatically identify and classify tetrads and quadruplexes.Structures from both sets were analysed using self-implemented programs along with DSSR software from the 3DNA suite (Lu et al.
From DSSR, we acquired the information about base pairs and stacking.I like the ONZ classification scheme: it is simple in concept yet provides a new perspective for the topologies of G-tetrads in intramolecular G4 structures. So I implemented the idea in DSSR v1.9.8-2019oct16, with this feature available via the -g4-onz option. Note that, according to the authors, is applicable to ONZ classifications of general types of tetrads and quadruplexes. The DSSR implementation of ONZ classifications, on the other hand, is strictly limited to G-tetrads in intramolecular G4 structures.The DSSR ONZ classification results match the ones reported in Figs. 1, 5, and 6 of the Popenda et al. For example, for (Fig.
Recently I noticed two new citations to. One is from the Yesselman et al. Article in Nature Nanotechnology, and the other is from the Wang et al. Article in International Journal of Molecular Sciences.Yesselman et al.
Has used DSSR in RNAMake for building the motif library. The relevant section is as follows:We processed each RNA structure to extract every motif with Dissecting the Spatial Structure of RNA ( DSSR)54 with the following command:x3dna-dssr –i file.pdb –o filedssr.outWe manually checked each extracted motif to confirm that it was the correct type, as DSSR sometimes classifies tertiary contacts as higher-order junctions and vice versa. For each motif collected from DSSR, we ran the X3DNA findpair and analyze programs to determine the reference frame for the first and last base pair of each motif to allow for the alignment between motifs:findpair file.pdb 2 /dev/null stdout analyze stdin & /dev/nullIt is worth noting the sentence that “ DSSR sometimes classifies tertiary contacts as higher-order junctions and vice versa.” Presumably. The authors are referring to the inclusion of ‘isolated canonical pairs’ in junctions by default in DSSR. Overall, the default DSSR settings follow the most common practice in RNA literature. In the meantime, I am aware that the community may not agree on every detail.
Thus DSSR provide many options (documented or otherwise) to cater for other potential use cases. See the and threads on the 3DNA Forum for two examples. In the long run, DSSR is likely to help consolidate RNA nomenclature that can be applied in a pragmatic, consistent manner.Note also that DSSR provides the reference frame of each identified base pair via the JSON option. Using 1ehz as an example, the following command provides detailed information about base pairs:x3dna-dssr -i=1ehz.pdb -json -more jq.pairsIn the 3dRNA 2.0 paper, DSSR is cited as below. This is the first time DSSR is integrated in the 3dRNA pipeline.The predicted structures are built from the sequence and secondary structure, while the former is obtained from their native structures fetched from PDB (and the latter is calculated from DSSR (Dissecting the Spatial Structure of RNA) 39.
3DNA is a 3D desktop enhancer that improves the way you work with Windows and the Web. You can choose from different 3D Add-on Worlds to explore and customize with 100's of themes and skies for an immersive and entertaining desktop. 3DNA works by overlaying the wallpaper area and easily lets you toggle between your 3D and 2D desktop with the click of your mouse.
The 3D Worlds also have toys to play with and integrated 3D games. You can move around easily, or simply teleport to different areas when you want to launch applications, open folders, speed-surf dozens of Web sites, or play music. Personalize each 3D World by hanging your digital photos on the walls by simply dragging them onto the picture frames.Within each World you have various areas to create links to your folders, files, and programs.
3DNA will even scan your system to create a custom set of links to get you started. Once you have selected the World you like, you can download additional user-created themes and skies or create your own to share.
The interface is intuitive, and there's an optional Tutorial World that walks you through the product. Overview3DNA Desktop is a Shareware software in the category Desktop developed by.The latest version of 3DNA Desktop is 1.1, released on. It was initially added to our database on.3DNA Desktop runs on the following operating systems: Windows.Users of 3DNA Desktop gave it a rating of 5 out of 5 stars.for 3DNA Desktop!
![](/uploads/1/2/7/6/127614135/582943999.jpg)