AMIGOS III: Pseudo-torsion Angle Visualization and Motif-based Structure Comparison of Nucleic Acids

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2022 May 13

PMID 35561202

Authors

Morgan Shine

Chengxin Zhang

Anna Marie Pyle

Affiliations

Soon will be listed here.

Abstract

Motivation: The 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.

Results: We 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.

Citing Articles

RNAtango: Analysing and comparing RNA 3D structures via torsional angles.

Mackowiak M, Adamczyk B, Szachniuk M, Zok T PLoS Comput Biol. 2024; 20(10):e1012500.

PMID: 39374268 PMC: 11486365. DOI: 10.1371/journal.pcbi.1012500.

PDC: a highly compact file format to store protein 3D coordinates.

Zhang C, Pyle A Database (Oxford). 2023; 2023.

PMID: 37010520 PMC: 10069377. DOI: 10.1093/database/baad018.

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