AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.
AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.
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DOI：
10.1093/bioinformatics/btac207
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发表时间：
2022-05-13
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核酸构象的完整描述涉及每个核苷酸的八个扭转角。为了简化这一描述，我们先前开发了核酸骨架的表示，其为每个核苷酸分配一对伪扭转角（由P和C4 π原子定义的η和θ;或由P和C1 π原子定义的η和θ）。Java程序AMIGOS II目前可用于计算RNA的eta和theta角，并基于eta和theta角进行基序搜索。然而，AMIGOS II缺乏解析DNA结构和计算η和θ矩形的能力。它对三维结构的可视化能力也很小，这使得用户难以解释计算结果。我们提出了AMIGOS III，一个PyMOL插件，它计算DNA和RNA结构的伪扭转角eta，theta，eta和theta，并根据这些角度进行基序搜索。与AMIGOS II相比，AMIGOS III提供了改进的RNA伪扭转角可视化和更快的核酸蠕虫数据库生成;它还引入了用于DNA和核酸蠕虫可视化的伪扭转角可视化。它集成到PyMOL中，可以轻松准备三级结构输入和直观地可视化所涉及的结构。 https://github.com/pylelab/AMIGOSIII. 补充数据可在在线生物信息学上获取。
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 C4ʹ atoms; or etaʹ and thetaʹ defined by P and C1ʹ 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 etaʹ and thetaʹ angles. It also has little visualization capacity for 3D structure, making it difficult for users to interpret the computational results. We present AMIGOS III, a PyMOL plugin that calculates the pseudo-torsion angles eta, theta, etaʹ and thetaʹ 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. https://github.com/pylelab/AMIGOSIII. Supplementary data are available at Bioinformatics online.