3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
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DOI：
10.12688/f1000research.18458.2
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发表时间：
2019-03
期刊：
影响因子：
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通讯作者：
Bernhard C. Thiel;Irene K. Beckmann;Peter Kerpedjiev;I. Hofacker
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文献类型：
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作者：
Bernhard C. Thiel;Irene K. Beckmann;Peter Kerpedjiev;I. Hofacker
我们提出forgi，一个Python库来分析RNA二级结构元件的三级结构。我们对RNA分子的描述集中在二级结构元素（茎、凸起和环）上。通过将圆柱体拟合到螺旋轴，这些元素被带入到粗粒度的3D结构表示中。与Biopython的集成允许处理全原子3D信息。forgi可以处理各种文件格式，包括点括号字符串，PDB和MMCIF文件。我们可以处理修饰的残基，缺失的残基，共折叠和多重折叠结构以及从任意位置开始的核苷酸数量。我们应用这个库的研究堆叠螺旋的交界处和伪结，并探讨如何在解决实验结构堆叠螺旋可以从同轴几何转向。
We present forgi, a Python library to analyze the tertiary structure of RNA secondary structure elements. Our representation of an RNA molecule is centered on secondary structure elements (stems, bulges and loops). By fitting a cylinder to the helix axis, these elements are carried over into a coarse-grained 3D structure representation. Integration with Biopython allows for handling of all-atom 3D information. forgi can deal with a variety of file formats including dotbracket strings, PDB and MMCIF files. We can handle modified residues, missing residues, cofold and multifold structures as well as nucleotide numbers starting at arbitrary positions. We apply this library to the study of stacking helices in junctions and pseudoknots and investigate how far stacking helices in solved experimental structures can divert from coaxial geometries.