4.5 Article

Symmetrization in the Calculation Pipeline of Gauss Function-Based Modeling of Hydrophobicity in Protein Structures

期刊

SYMMETRY-BASEL
卷 14, 期 9, 页码 -

出版社

MDPI
DOI: 10.3390/sym14091876

关键词

bioinformatics; bounding ellipsoid; fuzzy oil drop; globular protein; hydrophobic core; Jensen-Shannon divergence; principal component analysis; relative entropy; symmetry

资金

  1. Jagiellonian University Medical College [N41/DBS/000719]

向作者/读者索取更多资源

This paper demonstrates, discusses, and compares the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model for protein hydrophobicity density. The proposed modifications improve the accuracy, robustness, speed, and usability of the model, as confirmed by tests on various molecules with different shapes and functions.
In this paper, we show, discuss, and compare the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model, a coarse-grained model of density of hydrophobicity in proteins. In the FOD model, an input structure is enclosed in an axis-aligned ellipsoid called a drop. Two profiles of hydrophobicity are then calculated for its residues: theoretical (based on the 3D Gauss function) and observed (based on pairwise hydrophobic interactions). Condition of the hydrophobic core is revealed by comparing those profiles through relative entropy, while analysis of their local differences allows, in particular, determination of the starting location for the search for protein-protein and protein-ligand interaction areas. Here, we improve the baseline workflow of the FOD model by introducing symmetry to the hydrophobicity profile comparison and ellipsoid bounding procedures. In the first modification (FOD-JS), Kullback-Leibler divergence is enhanced with its Jensen-Shannon variant. In the second modification (FOD-PCA), the molecule is optimally aligned with the axes of the coordinate system via principal component analysis, and the size of its drop is determined by the standard deviation of all its effective atoms, making it less susceptible to structural outliers. Tests on several molecules with various shapes and functions confirm that the proposed modifications improve the accuracy, robustness, speed, and usability of Gauss function-based modeling of the density of hydrophobicity in protein structures.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.5
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

暂无数据
暂无数据