Recent Posts

1

Bug reports / Re: Missing DNA bases with negative residue number

« Last post by xiangjun on April 14, 2026, 02:12:50 pm »

Hi Mihir,

Great catch! I have successfully reproduced the issue. The bug is due to a parsing error within the wDSSR web interface. As shown below, the core DSSR engine itself handles negative residue numbering without any issues.

Execute the following command to see the enumeration:

Code: [Select]

x3dna-dssr mutate -i=9GBV.pdb --enum
An excerpt of the output is as follows:

# For each entry to be mutated, remove the leading #, and add to=base

# To mutate A.A9 to G in PDB entry 1ehz (tRNA):
#          #  chain=A name=A num=9  #9  A.A9
#       --->  chain=A name=A num=9 to=G

# To mutate B.DT19 to DC in PDB entry 355d (B-DNA):
#          #  chain=B name=DT num=19  #19  B.DT19, pairedNt=A.DA6
#       --->  chain=B name=DT num=19 to=DC

# Empty or comment (starting with #) lines are ignored.

#  chain=E name=DT num=-37  #1  E.DT-37, pairedNt=F.DA80
#  chain=E name=DG num=-36  #2  E.DG-36, pairedNt=F.DC79
#  chain=E name=DC num=-35  #3  E.DC-35, pairedNt=F.DG78
#  chain=E name=DC num=-34  #4  E.DC-34, pairedNt=F.DG77
#  chain=E name=DA num=-33  #5  E.DA-33, pairedNt=F.DT76
#  chain=E name=DT num=-32  #6  E.DT-32, pairedNt=F.DA75
#  chain=E name=DC num=-31  #7  E.DC-31, pairedNt=F.DG74
#  chain=E name=DA num=-30  #8  E.DA-30, pairedNt=F.DT73
#  chain=E name=DG num=-29  #9  E.DG-29, pairedNt=F.DC72
#  chain=E name=DA num=-28  #10  E.DA-28, pairedNt=F.DT71
#  chain=E name=DA num=-27  #11  E.DA-27, pairedNt=F.DT70
#  chain=E name=DA num=-26  #12  E.DA-26, pairedNt=F.DT69
#  chain=E name=DA num=-25  #13  E.DA-25, pairedNt=F.DT68
#  chain=E name=DC num=-24  #14  E.DC-24, pairedNt=F.DG67
......

We will resolve this wDSSR error shortly. In the meantime, please continue using the tool and report any further issues you encounter.

If it is an option for your workflow, I recommend installing the standalone version of DSSR on your computer and using the command-line interface directly.

Best regards,

Xiang-Jun

2

Bug reports / Re: Missing DNA bases with negative residue number

« Last post by mihir41@terpmail.umd.edu on April 14, 2026, 01:23:48 pm »

Hello Xiang-Jun,

I used the online tool for DNA mutation.

On the page https://web.x3dna-dssr.org/mutation

I entered PDB ID: "9GBV" in the left box. Then clicked on the "List all bases" button.

On the next page, I see bases listed for chains E (from resid number 0 to 121) and F (from resid number 0 to 80).

However, if you check the sequence map on the RCSB (https://www.rcsb.org/3d-view/9GBV), you would see that chain E residues range from -37 to 121, and chain F residues range from -78 to 80.

Please let me know if you need more information.

Best,
Mihir

3

Bug reports / Re: Missing DNA bases with negative residue number

« Last post by xiangjun on April 14, 2026, 11:34:06 am »

Hi,

Thank you for using our tools and for reaching out on the forum.

To help us investigate this further, could you please provide a step-by-step description of your workflow? Specifically, please include the exact commands or options you used so that we can reproduce the issue on our end. This will help us determine why the residues with negative numbers are not being displayed as expected.

Best regards,

Xiang-Jun

4

Bug reports / Missing DNA bases with negative residue number

« Last post by mihir41@terpmail.umd.edu on April 14, 2026, 08:51:15 am »

The PDB ID: 9GBV has 217 bp long dsDNA (Chain E & F). I plan to perform a mutation in some bases. But many of the bases are not displayed. Specifically, all the bases having a negative residue number are omitted by the portal.

5

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

« Last post by xiangjun on April 06, 2026, 02:02:29 pm »

Hi muha,

Thanks for posting on the Forum, and sorry for the late reply.

I understand your aim to build a unimolecular G-quadruplex model with alternating 5'-3', 3'-3', 3'-5', and 5'-5' linkages. DSSR does not have a built-in option for building such models, and I am not aware of any other software that can do this. In my understanding, this would require a combination of DSSR and a 3D manual editing tool to adjust the polarity of the linkages.

As far as analysis is concerned, DSSR should be able to identify G-tetrads, and may take each tract as broken chains. We need specific examples to show how DSSR should behave in these cases. I will consider modifying DSSR to handle these cases if feasible.

Best regards,

Xiang-Jun

6

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on April 01, 2026, 03:03:00 pm »

Hi Luca,

Thanks for your interest in 3DNA. You should now be able to see the download page on the 3DNA Forum.

Best regards,

Xiang-Jun

7

Site announcements / Staff Associate II (Computational Structural Biology) at Columbia University

« Last post by xiangjun on April 01, 2026, 01:36:23 pm »

The X3DNA-DSSR resource is at the forefront of structural bioinformatics, developing advanced tools for analyzing and modeling nucleic acid structures. We are seeking a highly motivated Staff Associate II to join our team and contribute to our next-generation analysis and visualization engine.

To see our resource in action, please visit wDSSR, our new web interface for dissecting and modeling 3D nucleic acid structures: https://web.x3dna-dssr.org/.

We are looking for a candidate with a strong scientific background in structural biology or bioinformatics and a desire to contribute to peer-reviewed publications through community-driven data analysis. We value individuals who are eager to learn, adapt to new technical challenges, and support the global research community.

For the full job description and to submit your application, please visit the official Columbia University posting:
https://apply.interfolio.com/183705

8

FAQs / Re: Where to download x3DNA

« Last post by 胡俊杰 on March 31, 2026, 02:15:19 am »

Hello!

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

9

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

10

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!