A novel measure to analyze protein structures: Aspect ratio in protein alpha shapes

被引：1

作者：

Bagci, Elife Z. ^{[1
]}

Senguler-Ciftci, Fatma ^{[2
]}

Ciftci, Unver ^{[3
]}

Demir, Ayhan ^{[4
]}

机构：

[1] Tekirdag Namik Kemal Univ, Dept Biol, Tekirdag, Turkey

[2] Univ Groningen, Dept Math, Groningen, Netherlands

[3] Tekirdag Namik Kemal Univ, Dept Math, Tekirdag, Turkey

[4] Turkish Hlth Inst TUSEB, Dept Projects Management & Support, Ankara, Turkey

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2021年 / 89卷 / 10期

关键词：

alpha shape; aspect ratio of tetrahedron; Delaunay triangulation; geometric descriptors; sphericity; RESIDUE PACKING; MACROMOLECULES; COMPUTATION;

D O I：

10.1002/prot.26148

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Proteins' three-dimensional (3D) structures are analyzed traditionally using geometric descriptors such as torsional angles and inter-atomic distances. In this study a measure that is borrowed from computational geometry, aspect ratio of each tetrahedron in alpha shapes of proteins, is utilized. This geometric descriptor differentiates alpha and beta structural classes of proteins when combined with principal components analysis. The method converts the structures of individual proteins, 3D coordinates of the atoms, to points on a plane. It has a high degree of accuracy in differentiating R and T structures of hemoglobin. Therefore, it is anticipated that the geometric measure can be used successfully in a method that is extended to solve classification problems in machine learning.

引用

页码：1270 / 1276

页数：7

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