Recent Posts

21

General discussions (Q&As) / Approach for building G-quadruplex models with 3'-3' and 5'-5'polarity inversion

« Last post by muha on March 26, 2026, 03:58:31 am »

Dear all,
I am working on the structural modeling of non-canonical G-quadruplexes (G4). Specifically, I am trying to build a monomolecular G4 model characterized by inversions of polarity (alternating 5'-3', 3'-3', 3'-5', and 5'-5' linkages) within the G-tracts.

I am looking for some guidance on how to build the starting structure: While DSSR is excellent at analyzing and rebuilding standard G4 topologies, i am not sure if it can handle these specific phosphodiester bond inversions.

Does DSSR have a built-in way to recognize and validate a chain that contains 3'-3' or 5'-5' linkages, or will it treat them as broken chains during analysis?
Are there specific commands in the latest DSSR releases (or via the mutate module) that allow for inverting the direction of a specific block of residues while maintaining the G-tetrad stacking geometry?

I am looking for a general methodology for handling these "inverted" backbone topologies in a way that remains compatible with subsequent Molecular Dynamics setups.
Once I find a stable workflow, I will be happy to summarize the steps for the community as per the forum guidelines.
Any suggestion is welcome!
Thank you for your time and for this useful resource.

Best

22

Site announcements / Announcing wDSSR: The Next-Generation Web Interface to X3DNA-DSSR

« Last post by xiangjun on March 17, 2026, 05:30:52 pm »

Dear 3DNA/DSSR Community,

We are thrilled to announce the official launch of wDSSR (https://web.x3dna-dssr.org/), the powerful new web interface to the X3DNA-DSSR analytical engine.

Developed by Drs. Shuxiang Li and Xiang-Jun Lu and supported by NIH grant R24GM153869, wDSSR represents a major leap forward from our highly popular 2019 Web 3DNA 2.0 framework. While Web 3DNA 2.0 has faithfully served the community for the analysis, visualization, and modeling of 3D nucleic acid structures, wDSSR was built from the ground up to take full advantage of modern web technologies and the latest DSSR backend capabilities.

A Modern, Streamlined Scientific Workflow
We have completely overhauled the user interface to provide a clean, intuitive, and task-driven experience. The core modeling and analysis tools are now seamlessly organized into a logical, single-word scientific workflow: Analyze, Rebuild, Model, Circularize, Mutate, Assemble, and Visualize.

Spotlight Feature: The "Assemble" Module
One of the most exciting upgrades is the newly renamed Assemble tab (formerly "Composite"). This advanced composite model builder allows you to effortlessly construct complex, higher-order models by linking any combination of nucleic acid duplexes or protein-DNA/RNA complexes. You can quickly connect up to six distinct target structures, ranging from simple linked A-DNA and B-DNA duplexes to large, protein-decorated structural assemblies.

Immediate Global Adoption
Although wDSSR has just launched, we are incredibly humbled to share that it is already seeing rapid worldwide adoption! According to recent network infrastructure data, the new interface is actively being used by researchers across North America, South America, Europe, and Asia. Within just a few days, we have recorded active sessions from prestigious institutions around the globe, including:

• The Weizmann Institute of Science in Israel
• Katholieke Universiteit Leuven in Belgium
• Queen's University in Canada
• Universidad Nacional Autonoma de Mexico (UNAM) in Mexico
• Emory University and the Wadsworth Centers Laboratories and Research in the United States
• Jawaharlal Nehru University and the China Education and Research Network in Asia

How to Cite
While a dedicated paper for wDSSR is currently in preparation, researchers should cite the server using its URL (https://web.x3dna-dssr.org/) alongside the 2019 Web 3DNA 2.0 paper and the foundational 2015 DSSR paper. Full details and funding acknowledgements can be found on our newly consolidated About page.

We invite you all to try out the new wDSSR platform! As always, your feedback is invaluable to us, and we encourage you to share your thoughts, questions, and structural models via the newly updated Questions & Feedback link in the wDSSR footer.

Happy modeling!

23

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on February 19, 2026, 09:29:26 am »

Hi Luca,

You should now have access to the Downloads section. To prevent spam, we manually monitor and verify all new registrations. This is a one-time process; now that you are verified, you can download the 3DNA software and post questions here in the forum.

Best regards,

Xiang-Jun

24

FAQs / Re: Where to download x3DNA

« Last post by Luca_Maggi on February 19, 2026, 03:33:57 am »

Hello!

Same here! I have received the e-mail confirming the registration but still don't see the download section.
Could you please give me access to that.

Many Thanks

Luca

25

General discussions (Q&As) / MOVED: Looking for a way to speed up do_x3dna process.

« Last post by xiangjun on February 15, 2026, 11:16:07 pm »

This topic has been moved to MD simulations.

http://forum.x3dna.org/index.php?topic=1060.0

26

MD simulations / Re: Looking for a way to speed up do_x3dna process.

« Last post by xiangjun on February 15, 2026, 11:15:42 pm »

Hi Karn,

Thanks for posting on the 3DNA Forum. Since you are using do_x3dna, Dr. Kumar (@rkumar) is the best person to answer your question. I've move this thread to MD simulations section which is more relevant to MD simulations. Hopefully, he will chime in soon.

Best regards,

Xiang-Jun

27

MD simulations / Looking for a way to speed up do_x3dna process.

« Last post by Karn4132 on February 15, 2026, 12:12:04 pm »

Hello,

I'm a new user of do_x3dna and I've been trying to find the helical parameters of the damaged DNA - Protein complex.
I found the issue that sometimes - x3dna does not detect the damaged bp, so I tried adding -ref at the end of the command.|

do_x3dna -f ../new.xtc -s ../new.pdb -ref

Currently, this line of command seems to work perfectly.
However, by using the referrence structure for the calculation, it takes much longer than before to finish the process.

Is this a normal outcome for not using the base pair parameter of the trajectory?
It is worth to mention that my trajectory is pretty long and the old process actually took quite a while to finish. The new code made the calculation even longer than I expected.

Karn 

28

MD simulations / Re: Clarification on how DNA radius is computed from 3DNA/DSSR

« Last post by xiangjun on February 03, 2026, 09:25:43 am »

Hi Mamta,

Thanks for using 3DNA and for posting your question on the 3DNA Forum.

3DNA performs a least-squares fit of linear global helical axes using equivalent C1' and RN9/YN1 atom pairs along each strand of a DNA duplex. It then calculates mean and deviation of helix radius based on P, O4', and C1' atoms. Of course, the linear global helical axes is only meaningful when the DNA duplex is not strongly distorted. You may also want to check Curves+ for deriving curvilinear helical axes.

Using 355d as an example, running 3DNA as below:

find_pair 355d.pdb | analyze

You will get an output file 355d.out, which contains the following content:

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix:    -0.1269   -0.2753   -0.9530
HETATM 9998  XS    X X 999      17.536  25.713  25.665
HETATM 9999  XE    X X 999      12.911  15.677  -9.080
Average and standard deviation of helix radius:
      P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)

You can extract the two HETATM lines into the original PDB file, and draw a line between them to visualize the global helical axis (in PyMOL, for example).

The underling algorithm is based on the NewHelix/FreeHelix program, and you can check the implementation details in the 3DNA source code.

Hope this helps.

Best regards,

Xiang-Jun

29

MD simulations / Clarification on how DNA radius is computed from 3DNA/DSSR

« Last post by Mamta on February 03, 2026, 08:21:48 am »

Dear Xiang-Jun,
I am using 3DNA to analyze DNA structures from molecular-dynamics simulations.
I get the standard 3DNA output files with base-pair and helical axis information.

I want to calculate the DNA radius from these 3DNA results.
Could you please tell me:

Which output values or parameters from 3DNA should be used to compute the DNA radius, and how exactly should it be calculated from the 3DNA analysis?

Thank you.

Best regards,
Mamta Yadav

30

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on January 11, 2026, 08:01:28 pm »

Hi,

You should now be able to see the Download section. Note that the current version of DSSR is distributed by the Columbia Technology Ventures (CTV).


Thanks for your interested in 3DNA/DSSR. If you have any questions, please do not hesitate to post them on the Forum.

Best regards,

Xiang-Jun