一种新的双向再平衡策略,用于识别碳化位
Linjun Chen1, Xiao-Yuan Jing2,3,4, Yaru Hao1
1School of Computer Science, Wuhan University, Wuhan, China.
BMC bioinformatics
|November 14, 2023
概括
预测蛋白质碳化对于疾病管理至关重要. 本研究介绍了Carsite_AGan,这是一种使用注意力和生成对抗网络的新方法,以有效地解决蛋白质碳化数据中的类不平衡,显著提高预测准确性.
科学领域:
- 生物化学 生化学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 蛋白质碳化是一种与衰老和疾病相关的不可逆转的翻译后修饰.
- 准确预测蛋白质碳化位点对于临床决策和了解蛋白质功能至关重要.
- 现有的预测方法与高度类不平衡的数据集作斗争,其中非碳化站点数量远远超过碳化站点.
研究的目的:
- 开发一种新的计算策略,用于准确识别蛋白质碳化位.
- 为了解决蛋白质碳化数据集中普遍存在的显著类失衡问题.
- 为了提高蛋白质碳化预测模型的有效性.
主要方法:
- 提出 Carsite_AGan,这是一个双向再平衡策略,利用注意力机制和生成对抗网络 (GAN).
- 实施了基于注意力的低样本技术,以选择重要的非碳化位.
- 采用基于GAN的过量采样方法来生成现实的碳化位点样本.
- 使用非线性支向量机分类器进行最终站点识别.
主要成果:
- Carsite_AGan有效地处理蛋白质碳化数据中的类不平衡.
- 注意力技术成功地确定了重要的非碳化位.
- GANs生成高可行性碳化位点样本.
- 拟议的方法显著优于现有的重新采样技术.
结论:
- 开发的Carsite_AGan方法在识别蛋白质碳化位点方面提供了显著的改进.
- 使用CarSite_AGan重新采样蛋白质碳化数据可以提高预测的准确性.
- 这种方法为临床应用和蛋白质碳基化进一步研究提供了一个有前途的工具.
更多相关视频
07:16Resin-Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation
Published on: June 21, 2021
1.8K
12:11Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
Published on: February 27, 2020
6.9K
相关概念视频
Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
Allosteric Proteins-ATCase
5.8K
Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.8K
Carbocations
11.3K
Carbocations are one of the reaction intermediates formed during several nucleophilic substitutions or elimination reactions. A carbocation is an electron-deficient species with the central carbon atom having six electrons and three bonded atoms. The central carbon in a carbocation is sp2 hybridized with trigonal planar geometry. It has an empty p orbital perpendicular to the plane of the structure that can accept electrons. Thus, carbocations act as strong electrophiles and may react with any...
11.3K
Titrimetric Methods: Types and Commonly Used Strategies
938
In chemistry, titrimetric methods are broadly classified into three types: volumetric, gravimetric, and coulometric. Volumetric titrations involve measuring the volume of a titrant of known concentration that is required to react completely with an analyte. In gravimetric titrations, the standard solution reacts with the analyte to form an insoluble precipitate, which is filtered, dried, and weighed. In coulometric titrations, current is applied to an electrochemical reaction until the reaction...
938
Double Resonance Techniques: Overview
218
Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or radiofrequency pulses to manipulate and observe two distinct nuclear spins. One important application of double resonance is spin decoupling, which selectively suppresses coupling with one type of nucleus while observing the NMR signal from another nucleus, simplifying the spectrum and enhancing resolution.
Spin decoupling is usually achieved by...
Spin decoupling is usually achieved by...
218
¹³C NMR: ¹H–¹³C Decoupling
1.1K
The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
1.1K
