使用机器学习和深度学习方法对真菌糖转移酶的分类和功能预测
Alejandro Jose Gomez-Garcia1, Jorge Humberto Ramirez-Prado1
1Biotechnology Unit, Centro de investigación Científica de Yucatán, A. C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida, Yucatán 97205, Mexico.
Fungal genetics and biology : FG & B
|November 7, 2025
概括
这项研究使用机器学习来分类糖系转移酶 (GTs),这些酶对生物多样性至关重要. 将结构和生化数据与深度学习相结合,为这些酶提供了更全面,数据驱动的分类系统.
科学领域:
- 酶学 是一种酶学.
- 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:
- 糖转移酶 (GTs) 是催化糖转移的重要酶,在生物系统中创造结构多样性.
- 现有的GT分类系统由于酶变异性而复杂,阻碍了模式识别.
- 要了解GT结构-功能关系,需要采用统一的方法.
研究的目的:
- 开发一种新的,数据驱动的糖系转移酶 (GTs) 分类系统.
- 通过使用机器学习整合结构和生化特征来发现功能模式.
- 克服传统的,不同的分类方法的局限性.
主要方法:
- 利用了88种真菌物种的3340个GT的数据集.
- 采用卷积变异自编码器 (CVAE) 来处理3D折叠和氨基酸数据到五个向量.
- 丰富的CVAE向量与衍生变量,并应用k-means集群用于模式识别.
主要成果:
- 基于丰富数据的聚类显示出比仅结构数据更高的连贯性.
- 综合方法促进了对GT关系的全面理解.
- 该CVAE模型与生化和结构变量相结合,产生了一个互补的分类系统.
结论:
- 该方法比传统的基于序列的GT研究有显著的进步.
- 深度学习,特别是CVAE,增强了对GT及其生物功能的研究.
- 这种综合,数据驱动的方法提供了更完整的GT分类.
相关概念视频
Classification of Neurotransmitters
5.0K
Neurotransmitters play a crucial role in the communication between neurons in the autonomic nervous system. Neurons in the autonomic nervous system can be cholinergic or adrenergic depending on the neurotransmitters synthesized. Cholinergic neurons use acetylcholine as their primary neurotransmitter. This includes all the preganglionic fibers of the sympathetic and pre- and postganglionic fibers of the parasympathetic nervous systems. In addition, neurons of the somatic nervous system also use...
5.0K
Overview of Fungi
1.5K
Fungi are a diverse group of eukaryotes more closely related to animals than other eukaryotes. Fungal cell walls comprise chitin, a polysaccharide that provides structural strength, and glucans, which contribute to flexibility and integrity. Other polysaccharides, such as mannans and galactosans, may supplement or replace chitin in some fungi. These adaptations, along with their preference for acidic environments and tolerance for high osmotic pressure, enable fungi to thrive in various...
1.5K
Fungal Group Zygomycota
965
Zygomycota, previously classified as a distinct fungal group, are primarily terrestrial, saprophytic molds that play a crucial role as decomposers. Recent phylogenetic studies have revealed that these fungi are now divided into two major clades — Mucoromycota, which includes many symbiotic species, and Zoopagomycota, which primarily consists of parasitic and pathogenic fungi. These groups exhibit distinct ecological roles and reproductive strategies while sharing key structural and...
965
Classification of Systems-I
543
Linearity is a system property characterized by a direct input-output relationship, combining homogeneity and additivity.
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:
543
Methods of Classification and Identification
972
Bacterial identification relies on a diverse array of techniques to classify and understand microorganisms, each tailored to uncover specific characteristics. Traditional morphological approaches, while still valuable, are limited for closely related or structurally simple organisms. Modern methods integrate biochemical, serological, genetic, and advanced molecular tools to achieve greater accuracy.Morphological and Biochemical TechniquesMorphological characteristics, such as cell shape and...
972
Fungal Phylum Basidiomycota
841
Basidiomycota is a diverse phylum of fungi that includes ecologically significant decomposers such as white rot fungi, symbionts like mycorrhizal fungi, plant pathogens such as rusts and smuts, and edible species like Agaricus bisporus (the common button mushroom). These fungi play crucial roles in nutrient cycling, symbiotic relationships, and even human health. Their defining feature is the basidium, a microscopic club-shaped structure responsible for producing basidiospores.Fruiting Bodies...
841


