ArticleBioinformatics (Oxford, England)2022
AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Genome assembly and Full-length transcriptome of Malabar Red Snapper, Lutjanus malabaricus.Scientific data · 2026Article
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- Prevalence of dual-donating amines in key regions of functional RNAs.RNA (New York, N.Y.) · 2025Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- PDC: a highly compact file format to store protein 3D coordinates.Database : the journal of biological databases and curation · 2023Article
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3 authors.
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Abstract
motivationThe full description of nucleic acid conformation involves eight torsion angles per nucleotide. To simplify this description, we previously developed a representation of the nucleic acid backbone that assigns each nucleotide a pair of pseudo-torsion angles (eta and theta defined by P and C4' atoms; or eta' and theta' defined by P and C1' atoms). A Java program, AMIGOS II, is currently available for calculating eta and theta angles for RNA and for performing motif searches based on eta and theta angles. However, AMIGOS II lacks the ability to parse DNA structures and to calculate eta' and theta' angles. It also has little visualization capacity for 3D structure, making it difficult for users to interpret the computational results.
resultsWe present AMIGOS III, a PyMOL plugin that calculates the pseudo-torsion angles eta, theta, eta' and theta' for both DNA and RNA structures and performs motif searching based on these angles. Compared to AMIGOS II, AMIGOS III offers improved pseudo-torsion angle visualization for RNA and faster nucleic acid worm database generation; it also introduces pseudo-torsion angle visualization for DNA and nucleic acid worm visualization. Its integration into PyMOL enables easy preparation of tertiary structure inputs and intuitive visualization of involved structures. AVAILABILITY AND IMPLEMENTATION: https://github.com/pylelab/AMIGOSIII. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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