Conformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group.
Conformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group.
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DOI：
10.1093/nar/gkw717
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发表时间：
2016-09-30
影响因子：
14.9
通讯作者：
Jaskolski M
中科院分区：
文献类型：
--
作者：
Kowiel M;Brzezinski D;Jaskolski M
大分子结构的精细化通常借助于几何约束形式的先前立体化学知识。这种限制也用于核酸的柔性糖-磷酸骨架。然而，最近的高精度的DNA结构研究表明，磷酸键角可能有不足的描述，在现有的立体化学词典。本文分析了剑桥结构数据库中磷酸二酯基团的成键变形，将所研究的片段归类为六类构象相关的片段，并提出了一套修正的O-P-O键角和键距的约束条件。建议的限制已被积极验证对数据从核酸数据库和超高分辨率Z-DNA结构的蛋白质数据库。此外，PO 4几何形状的手动分类与机器学习方法自动发现的几何聚类进行了比较。机器学习聚类分析为自动发现分子几何隐藏模式的聚类算法的一般应用提供了有用的见解和实际例子。最后，我们描述了一个公共域的Web服务器的自动生成建议的限制的实现和应用。
The refinement of macromolecular structures is usually aided by prior stereochemical knowledge in the form of geometrical restraints. Such restraints are also used for the flexible sugar-phosphate backbones of nucleic acids. However, recent highly accurate structural studies of DNA suggest that the phosphate bond angles may have inadequate description in the existing stereochemical dictionaries. In this paper, we analyze the bonding deformations of the phosphodiester groups in the Cambridge Structural Database, cluster the studied fragments into six conformation-related categories and propose a revised set of restraints for the O-P-O bond angles and distances. The proposed restraints have been positively validated against data from the Nucleic Acid Database and an ultrahigh-resolution Z-DNA structure in the Protein Data Bank. Additionally, the manual classification of PO4 geometry is compared with geometrical clusters automatically discovered by machine learning methods. The machine learning cluster analysis provides useful insights and a practical example for general applications of clustering algorithms for automatic discovery of hidden patterns of molecular geometry. Finally, we describe the implementation and application of a public-domain web server for automatic generation of the proposed restraints.
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影响因子：
14.9
作者：
Jakób M;Kołodziejczyk R;Orłowski M;Krzywda S;Kowalska A;Dutko-Gwóźdź J;Gwóźdź T;Kochman M;Jaskólski M;Ozyhar A
通讯作者：
Ozyhar A
影响因子：
3.5
作者：
Deller MC;Rupp B
通讯作者：
Rupp B
DOI：
10.1107/s0907444995011115
发表时间：
1996-01-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Parkinson, G;Vojtechovsky, J;Berman, HM
通讯作者：
Berman, HM
DOI：
10.1107/s0108768102003324
发表时间：
2002-06-01
影响因子：
1.9
作者：
Bruno, IJ;Cole, JC;Taylor, R
通讯作者：
Taylor, R
影响因子：
2.9
作者：
Raczynska, Joanna E.;Wlodawer, Alexander;Jaskolski, Mariusz
通讯作者：
Jaskolski, Mariusz