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Analyzing Change in Protein Stability Associated with Single Point Deletions in a Newly Defined Protein Structure Database.
Journal of Proteome Research ( IF 4.4 ) Pub Date : 2019-02-18 , DOI: 10.1021/acs.jproteome.9b00048
Anupam Banerjee , Yaakov Levy 1 , Pralay Mitra
Affiliation  

Protein backbone alternation due to insertion/deletion or mutation operation often results in a change of fundamental biophysical properties of proteins. The proposed work intends to encode the protein stability changes associated with single point deletions (SPDs) of amino acids in proteins. The encoding will help in the primary screening of detrimental backbone modifications before opting for expensive in vitro experimentations. In the absence of any benchmark database documenting SPDs, we curate a data set containing SPDs that lead to both folded conformations and unfolded state. We differentiate these SPD instances with the help of simple structural and physicochemical features and eventually classify the foldability resulting out of SPDs using a Random Forest classifier and an Elliptic Envelope based outlier detector. Adhering to leave one out cross validation, the accuracy of the Random Forest classifier and the Elliptic Envelope is of 99.4% and 98.1%, respectively. The newly defined database and the delineation of SPD instances based on its resulting foldability provide a head start toward finding a solution to the given problem.

中文翻译:

在新定义的蛋白质结构数据库中分析与单点缺失相关的蛋白质稳定性变化。

由于插入/缺失或突变操作而引起的蛋白质主链交替经常导致蛋白质基本生物物理特性的改变。拟议的工作旨在编码与蛋白质中氨基酸的单点缺失(SPD)相关的蛋白质稳定性变化。在选择昂贵的体外实验之前,编码将有助于有害骨架修饰的初步筛选。在没有任何基准数据库记录SPD的情况下,我们整理一个包含SPD的数据集,这些SPD导致折叠的构象和未折叠的状态。我们借助简单的结构和物理化学特征来区分这些SPD实例,并最终使用随机森林分类器和基于椭圆信封的离群值检测器对SPD产生的可折叠性进行分类。坚持遗漏的交叉验证,Random Forest分类器和椭圆形信封的准确度分别为99.4%和98.1%。新定义的数据库和基于SPD实例可折叠性的描述为找到给定问题的解决方案提供了开端。
更新日期:2019-02-19
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