Recent Posts

1

General discussions (Q&As) / Re: Calculate torsion angles of the DNA, without taking into account the bases

« Last post by xiangjun on September 10, 2022, 09:38:10 pm »

Hi Andrea,

DSSR Pro can do what you want very easily, especially in combination with the --json option. See No more grant funding for 3DNA/DSSR.

Base atoms have always been necessary for the identification of nucleotides in order to calculate base-pair and backbone parameters in 3DNA v2.x, including the command you mentioned: analyze -t=torsions.out. However, since 3DNA v2.x is open source for academic uses, you can modify it to meet your needs.

Best regards,

Xiang-Jun

2

General discussions (Q&As) / Calculate torsion angles of the DNA, without taking into account the bases

« Last post by Andrea R on September 10, 2022, 06:48:52 pm »

Dear Dr. Xiang-Jun Lu,

I used versions of 3DNA earlier than the 2018 versions some time ago, in those versions it was possible to calculate the torsion angles of the sugar-phosphate backbone of DNA, without taking into account the bases, with the following command:

analyze -t = name.tor name.pdb

However in the new versions, this task is not possible anymore, it is necessary to have the nitrogenous bases or at least   N1, C2 or N9, C4 atoms. 

I was wondering if there is a new instruction or way to do that, because it would shorten my work route considerably. One of my study purposes is the optimized fragments of the Sugar-Phosphate Backbone, in these fragments the nitrogenous bases of the DNA are eliminated and replaced by a hydrogen (position N1 or N9) as shown in file attached .

Thank you very much,

Andrea R.

3

Site announcements / Re: Clarification on DSSR licensing

« Last post by xiangjun on August 11, 2022, 09:24:51 am »

Hi Dr. Baulin,

is it safe to freely use the old DSSR version for academic use according to the old license?

Yes. Keep in mind that such outdated versions are no longer supported or maintained.

Best regards,

Xiang-Jun

4

Site announcements / Re: Clarification on DSSR licensing

« Last post by febos on August 11, 2022, 07:34:37 am »

Hi Dr. Lu!

About two years ago I downloaded DSSR version 2.0 for academic use and since then I built some work using the tool. Only now have I found out that the newest DSSR versions are not freely available anymore. And now I have a question - is it safe to freely use the old DSSR version for academic use according to the old license?

Thank you!

Best regards,
Eugene Baulin

5

General discussions (Q&As) / relationship between the two base-pair coordinate frames

« Last post by zhao on May 08, 2022, 06:36:38 am »

Hi Xiangjun:
     When we use 3DNA to analyze the tertiary structure of RNA, we get the local base pair parameters and simple base pair parameters, and know that different base-pair coordinate frames lead to different results. We would like to know what is the relationship between the two base-pair coordinate frames, but we have not found anything after searching. Could you help us solve this problem?

Zhao

6

Site announcements / Re: Download instructions

« Last post by wdz-victor on March 25, 2022, 01:09:21 am »

Hello everyone, how can I get the old version of the program, or how can the new version 2.4 program run through the pymol script. (No x3dna-dssr.exe found in the new program)

7

General discussions (Q&As) / Rebuild with backbone from single-stranded .par file

« Last post by nicalleb on March 21, 2022, 07:39:35 am »

Dear,

I would like to rebuild a stacked nucleobases structure from a .par file (with the 6  base-step parameters, see in attachment). This .par file was obtained by analyzing a single-stranded GTT stack (PDB file) with the command "find pair". If I rebuild my structure from this .par file with the following command :

rebuild -atomic bp_step.par test_rebuild.pdb

I get a structure without backbone and I need the backbone in subsequent calculations.

With the "Rebuilding" module of the online version of X3DNA, I know it is possible to have a structure with backbone, even starting with a .par file for a single-strand (containing only 6 local base-step parameters)

Is it also possible in command line (with the downloaded version of the software) and if so, how ?


Thank you in advance,

Nicolas Callebaut

8

RNA structures (DSSR) / Re: create a multiple copy from a building block with DSSR-pro

« Last post by xiangjun on January 29, 2022, 12:07:35 pm »

Hi Amir,

Thanks for your support of the DSSR project by purchasing an academic license. As noted in the announcement post "No more grant funding for 3DNA/DSSR", I am committed (now in my 'spare time') to making DSSR a brand that stands for quality and value. I strive to provide paying users the best support they can expect from a software product. The objective is to ensure that the time and effort saved by using DSSR well outweighs the licensing charge, particularly the $1,000 one-time fee for academic users. As an example, did you realize how much time and work you save by getting DSSR up and running vs other software tools you are familiar with?

Now, let's get back to your precise question. I understand what you mean, but the information you supplied is insufficient to demonstrate the problem. Could you provide a minimum example that can reproduce exactly what you want to achieve?

DSSR Pro users, particularly those in the (pharmaceutical) industry, are oftentimes concerned about the data they are willing to share with the public. Thus I've been assisting them via email, phone, WeChat, or Zoom: whatever is convenient and effective. We can keep the topic going on the Forum, or you may wish to go private.

Best regards,

Xiang-Jun

9

RNA structures (DSSR) / create a multiple copy from a building block with DSSR-pro

« Last post by amirtaghavi on January 28, 2022, 11:23:34 am »

Hello Dr. Lu,

I am using the DSSR-pro and the work flow you provided to create a multiple copy of a 3bp RNA (attached), I was wondering if it is possible to use the DSSR to create the lost backbone connections.

Thanks,
Amir

x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb

x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair -o=ref-conn.pdb

x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb' -o=temp1.pdb

x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb

x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb' -o=duplicate-model.pdb

10

Site announcements / DSSR-enabled innovative PyMOL schematics in the covers of the RNA Journal

« Last post by xiangjun on December 20, 2021, 11:31:10 am »

The DSSR-PyMOL schematics have been featured in all 12 cover images (January to December) of the RNA Journal in 2021. Moreover, the January 2022 issue of RNA continues to highlight DSSR-enabled schematics (see the note below). In the current Covid-19 pandemic, this cover seems to be a fit for the upcoming Christmas holiday season.

Ebola virus matrix protein octameric ring (PDB id: 7K5L; Landeras-Bueno S, Wasserman H, Oliveira G, VanAernum ZL, Busch F, Salie ZL, Wysocki VH, Andersen K, Saphire EO. 2021. Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form. Cell Rep 35: 108986). The Ebola virus matrix protein (VP40) forms distinct structures linked to distinct functions in the virus life cycle. VP40 forms an octameric ring-shaped (D4 symmetry) assembly upon binding of RNA and is associated with transcriptional control. RNA backbone is displayed as a red ribbon; block bases use NDB colors: A—red, G—green, U—cyan; protein is displayed as a gold ribbon. Cover image provided by the Nucleic Acid Database (ndbserver.rutgers.edu). Image generated using DSSR and PyMOL (Lu XJ. 2020. _Nucleic Acids Res_ *48*: e74).

Thanks to Dr. Cathy Lawson at the NDB for generating these cover images using DSSR and PyMOL for the RNA Journal. I'm gratified that the 2020 NAR paper is explicitly acknowledged: it's the first time I've published as a single author in my scientific career.

Did you know that you can easily generate similar DSSR-PyMOL schematics via the http://skmatic.x3dna.org/ website? It is "simple and effective", "good for teaching", and has been highly recommended by Dr. Quentin Vicens (CU Denver) in FacultyOpinions.com.


The 12 PDB structures illustrated in the 2021 covers are:

• January 2021 "iMango-III fluorescent aptamer (PDB id: 6PQ7; Trachman III RJ, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferre-D'Amare AR. 2019. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Cryst F 75: 547). Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold)."
• February 2021 "Human adenosine deaminase (E488Q mutant) acting on dsRNA (PDB id: 6VFF; Thuy-Boun AS, Thomas JM, Grajo HL, Palumbo CM, Park S, Nguyen LT, Fisher AJ, Beal PA. 2020. Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa532). Adenosine deaminase enzymes convert adenosine to inosine in duplex RNA, a modification that strongly affects RNA structure and function in multiple ways."
• March 2021 "Hepatitis A virus IRES domain V in complex with Fab (PDB id: 6MWN; Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. 2019. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun 10: 3629)."
• April 2021 "Mouse endonuclease V in complex with 23mer RNA (PDB id: 6OZO; Wu J, Samara NL, Kuraoka I, Yang W. 2019. Evolution of inosine-specific endonuclease V from bacterial DNase to eukaryotic RNase. Mol Cell 76: 44). Endonuclease V cleaves the second phosphodiester bond 3′ to a deaminated adenosine (inosine). Although highly conserved, EndoV change substrate preference from DNA in bacteria to RNA in eukaryotes."
• May 2021 "Manganese riboswitch from Xanthmonas oryzae (PDB id: 6N2V; Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG. 2019. Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nat Commun 10: 4304). Bacterial manganese riboswitches control the expression of Mn2+ homeostasis genes. Using FRET, it was shown that an extended 4-way-junction samples transient docked states in the presence of Mg2+ but can only dock stably upon addition of submillimolar Mn2+."
• June 2021 "Sulfolobus islandicus Csx1 RNase in complex with cyclic RNA activator (PDB id: 6R9R; Molina R, Stella S, Feng M, Sofos N, Jauniskis V, Pozdnyakova I, Lopez-Mendez B, She Q, Montoya G. 2019. Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas. Nat Commun 10: 4302). CRISPR-Cas multisubunit complexes cleave ssRNA and ssDNA, promoting the generation of cyclic oligoadenylate (cOA), which activates associated CRISPR-Cas RNases. The Csx1 RNase dimer is shown with cyclic (A4) RNA bound."
• July 2021 "M. tuberculosis ileS T-box riboswitch in complex with tRNA (PDB id: 6UFG; Battaglia RA, Grigg JC, Ke A. 2019. Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Nat Struct Mol Biol 26: 1106). T-box riboregulators are a class of cis-regulatory RNAs that govern the bacterial response to amino acid starvation by binding, decoding, and reading the aminoacylation status of specific transfer RNAs."
• August 2021 "CAG repeats recognized by cyclic mismatch binding ligand (PDB id: 6QIV; Mukherjee S, Blaszczyk L, Rypniewski W, Falschlunger C, Micura R, Murata A, Dohno C, Nakatan K, Kiliszek A. 2019. Structural insights into synthetic ligands targeting A–A pairs in disease-related CAG RNA repeats. Nucleic Acids Res 47:10906). A large number of hereditary neurodegenerative human diseases are associated with abnormal expansion of repeated sequences. RNA containing CAG repeats can be recognized by synthetic cyclic mismatch-binding ligands such as the structure shown."
• September 2021 "Corn aptamer complex with fluorophore Thioflavin T (PDB id: 6E81; Sjekloca L, Ferre-D'Amare AR. 2019. Binding between G quadruplexes at the homodimer interface of the Corn RNA aptamer strongly activates Thioflavin T fluorescence. Cell Chem Biol 26: 1159). The fluorescent compound Thioflavin T, widely used for the detection of amyloids, is bound at the dimer interface of the homodimeric G-quadruplex-containing RNA Corn aptamer."
• October 2021 "Cas9 nuclease-sgRNA complex with anti-CRISPR protein inhibitor (PDB id: 6JE9; Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, et al. 2019. Structures of Neisseria meningitidis Cas9 complexes in catalytically poised and anti-CRISPR-inhibited states. Mol Cell 76: 938­–952.e5). Nme1Cas9, a compact nuclease for in vivo genome editing. AcrIIC3 is an anti-CRISPR protein inhibitor."
• November 2021 "Two-quartet RNA parallel G-quadruplex complexed with porphyrin (PDB id: 6JJI; Zhang Y, Omari KE, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D. 2020. Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Nucleic Acids Res 48: 9886–9898)."
• December 2021 "Structure of S. pombe Lsm1–7 with RNA, polyuridine with 3' guanosine (PDB id: 6PPV; Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE. 2020. Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes. RNA 26: 1400–1413). Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1–7 complex initiates mRNA decay, while the nuclear Lsm2–8 complex acts as a chaperone for U6 spliceosomal RNA."