Work

gmx-dssna

Year: 2026

Type: software

Abstract: DSSNA (Define Spatial Structure of Nucleic Acids) DSSNA is an open-source tool for automated analysis of nucleic acid secondary and tertiary structure from atomic coordinates, including time-series data from molecular dynamics (MD) simulations. Inspired by the conceptual framework of X3DNA/DSSR, DSSNA provides an independent implementation integrated with GROMACS-based workflows. Features: Base-pair detection: Identifies canonical and non-canonical base pairs using geometric criteria Base-stacking analysis: Detects stacking interactions via overlap-area or geometric methods Helical parameters: Computes dinucleotide and helical step parameters Secondary structure annotation: Generates dot-bracket notation compatible with VARNA A-minor motif detection: Identifies and classifies A-minor interactions MD trajectory support: Analyzes time-dependent structural changes in nucleic acids GROMACS integration: Seamlessly works with GROMACS output formats

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.22912258

Authors: Gorelov, Sergey, Shvetsov, Alexey

Institutions: Peter the Great St. Petersburg Polytechnic University, Kurchatov Institute, Petersburg Nuclear Physics Institute

Language: English

Topic: RNA and protein synthesis mechanisms

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W7214101320

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