DSSNA — nucleic acids secondary/tertiary structure analysis tool for MD trajectories

Third party tools and files
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Dear GROMACS community,

I would like to share a tool that may be of interest to those simulating DNA and RNA systems.

DSSNA (Define Spatial Structure of Nucleic Acids) is an algorithm for automatic assignment of secondary and tertiary structure of nucleic acids from molecular dynamics trajectories. It works analogously to DSSP for proteins, but is specifically designed for the geometry and chemistry of DNA and RNA. The method identifies Watson-Crick and non-canonical base pairs, analyzes base stacking interactions, classifies helical regions, and recognizes common structural motifs such as hairpins, internal loops, bulges, and junctions. DSSNA processes full MD trajectories and computes time-resolved characteristics including occupancy and lifetime for base pairs and base-stacking interactions.

An article preprint with the detailed methodology and example of usage is available here: DSSNA: An Open-Source GROMACS Module for Automated Analysis of Nucleic Acid Secondary and Tertiary Structure in Molecular Dynamics Simulations.

A standalone DSSNA module is available at bio-pnpi / gmx-dssna · GitLab.

The module accepts standard trajectory formats and produces per-frame structure assignments.

I would be grateful for any feedback from the community, especially from users who regularly work with nucleic acid simulations. If there is interest, I would also be happy to discuss potential integration of DSSNA into GROMACS as a native analysis tool (similar to gmx dssp for proteins).

Best regards,

Sergey Gorelov

1 Like
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Hi this looks super useful.

I have a project wrapping up where I’d love to try this - I havn’t had a full dive into it yet, but could you tell me if it supports non-cannonical DNA residues?

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Thank you!

Yes, DSSNA supports non-standard DNA/RNA nucleotides (that’s what you meant if I understood you correctly). When analyzing nucleotides from the input file, DSSNA will look for the most similar standard nucleotide to classify them, since many motifs are defined only for standard nucleotides.