Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06511, USA.
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
Bioinformatics. 2022 May 13;38(10):2937-2939. doi: 10.1093/bioinformatics/btac207.
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.
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.
https://github.com/pylelab/AMIGOSIII.
Supplementary data are available at Bioinformatics online.
核酸构象的完整描述涉及每个核苷酸的八个扭转角。为了简化这个描述，我们之前开发了一种核酸骨架的表示方法，它为每个核苷酸分配一对伪扭转角（由 P 和 C4'原子定义的 eta 和 theta；或由 P 和 C1'原子定义的 eta'和 theta'）。目前有一个名为 AMIGOS II 的 Java 程序可用于计算 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 eta'和 theta'角的能力。它对 3D 结构的可视化能力也很有限，使用户难以解释计算结果。
我们提出了 AMIGOS III，这是一个 PyMOL 插件，它可以为 DNA 和 RNA 结构计算伪扭转角 eta、theta、eta'和 theta'，并基于这些角进行基序搜索。与 AMIGOS II 相比，AMIGOS III 为 RNA 提供了改进的伪扭转角可视化效果，并且可以更快地生成核酸蠕虫数据库；它还为 DNA 引入了伪扭转角可视化和核酸蠕虫可视化。它与 PyMOL 的集成使得准备三级结构输入和直观地可视化相关结构变得更加容易。
https://github.com/pylelab/AMIGOSIII。
补充数据可在 Bioinformatics 在线获得。
