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相关概念视频

Nucleic Acid Structure01:25

Nucleic Acid Structure

6.9K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
6.9K
Protein Networks02:26

Protein Networks

4.1K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.1K
Protein Complex Assembly02:41

Protein Complex Assembly

10.8K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
10.8K
Protein Organization01:24

Protein Organization

7.0K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
7.0K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.6K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.6K
Protein-protein Interfaces02:04

Protein-protein Interfaces

13.2K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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相关实验视频

Updated: Sep 9, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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基于图形学习的RNA-蛋白质复合结构评分

Zheng Jiang1, Ye Zhang1, Guipu Yang1

  • 1Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.

Journal of chemical theory and computation
|August 29, 2025
PubMed
概括
此摘要是机器生成的。

EGARPS+使用图形深度学习来评分RNA-蛋白质复杂结构,其性能优于CNN和统计潜力. 这种新方法改善了预测,特别是对于灵活的复合体,并有助于新的结构预测.

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

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相关实验视频

Last Updated: Sep 9, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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科学领域:

  • 计算生物学
  • 结构生物信息学
  • 结构生物学中的机器学习

背景情况:

  • 准确的评分功能对于预测RNA-蛋白质复杂结构至关重要.
  • 传统的方法难以实现形状的灵活性.
  • 卷积神经网络 (CNN) 是有前途的,但图形深度学习为生物分子任务提供了卓越的性能.

研究的目的:

  • 为RNA-蛋白质复合结构开发基于图形学习的新型评分功能.
  • 加强这些复合体内的分子间和分子内相互作用的评估.
  • 提高RNA蛋白结构预测的准确性和稳定性.

主要方法:

  • 提出了EGARPS+,一个使用等价图神经网络和注意力机制的图形学习算法.
  • 结合了新的序列,结构和交互特征来表示接口.
  • 开发了单独的分子间和分子内模块进行综合评估.

主要成果:

  • 在绑定和非绑定数据集上,EGARPS+的表现始终优于基于CNN的方法和统计潜力.
  • 该模型在具有显著形状变化,小接口和低结构相似性的复合体上表现出卓越的性能.
  • 在与RoseTTAFoldNA和AlphaFold3相结合时,EGARPS+增强了 de novo RNA- 蛋白质复合体的预测.

结论:

  • 图形深度学习,特别是EGARPS+,为评分RNA-蛋白质复杂结构提供了强大的方法.
  • 该模型能够处理复杂的案例并改进现有的预测工具,这凸显了其意义.
  • 解释性分析揭示了RNA与蛋白质相互作用中的保存动机和键的重要性.