HELANAL: A program to characterize helix geometry in proteins
HELANAL: A program to characterize helix geometry in proteins
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DOI：
10.1080/07391102.2000.10506570
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发表时间：
2000-04-01
影响因子：
4.4
通讯作者：
Velavan, R
中科院分区：
文献类型：
--
作者：
Bansal, M;Kumar, S;Velavan, R
详细分析螺旋的结构和位置依赖特征将有助于更好地理解球状蛋白的二级结构形成。在这里，我们描述了一种算法，该算法仅基于它们的c - α原子来量化蛋白质中螺旋的几何形状。Fortran程序HELANAL可以从PDB文件中提取螺旋，然后根据其局部结构特征，即局部螺旋扭曲和上升，虚拟扭转角，局部螺旋原点和连续的局部螺旋轴之间的弯曲角，将每个螺旋的整体几何形状表征为线性，弯曲或扭结。即使具有大曲率半径的螺旋也可以明确地识别为线性或弯曲。该程序还可以用来区分一个扭结螺旋和其他图案，如螺旋-环-螺旋或螺旋-转-螺旋（与一个单一的残留链接）与局部弯曲角度的帮助。除此之外，该程序还可以用于表征螺旋的开始和结束以及其他类型的二级结构。
A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.