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相关概念视频

Protein Organization01:24

Protein Organization

6.2K
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....
6.2K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.4K
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...
12.4K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.8K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.8K
Protein Networks02:26

Protein Networks

3.9K
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,...
3.9K
Protein and Protein Structure02:15

Protein and Protein Structure

78.2K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
78.2K
Protein and Protein Structures02:15

Protein and Protein Structures

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相关实验视频

Updated: Jun 2, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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PHIStruct:在低序列相似性设置下改善菌体与宿主相互作用的预测,使用结构感知蛋白质嵌入.

Mark Edward M Gonzales1,2, Jennifer C Ureta1,2,3, Anish M S Shrestha1,2

  • 1Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila 1004, Philippines.

Bioinformatics (Oxford, England)
|January 13, 2025
PubMed
概括

通过结构感知蛋白质嵌入,PHIStruct准确地预测菌体宿主. 这种计算工具的性能优于现有的方法,尤其是低序列相似性,推进了菌体与宿主相互作用的预测.

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相关实验视频

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科学领域:

  • 计算生物学是一种计算生物学.
  • 结构生物信息学 结构生物信息学
  • 微生物学 微生物学

背景情况:

  • 目前用于菌体与宿主相互作用预测的仅序列模型缺乏结构信息.
  • 这些模型中的蛋白质嵌入不捕捉宿主特异性的关键结构信息信号.

研究的目的:

  • 开发一种新的计算工具,PHIStruct,用于预测菌体宿主.
  • 将蛋白质结构信息纳入菌体与宿主相互作用预测模型.

主要方法:

  • PHIStruct使用来自SaProt蛋白质语言模型的结构意识嵌入.
  • 在PHIStruct中的多层感知子预测基于受体结合蛋白结构意识嵌入的宿主属 (ESKAPEE).

主要成果:

  • 与现有工具相比,PHIStruct表现出卓越的精度和回忆能力.
  • 它在各种信心门和序列相似性中获得了最高和最稳定的F1分数.
  • 当序列相似性低于40%时,PHIStruct显示了与非结构信息化的ML工具相比,类平均F1的7%-9%的增加,以及与BLASTp相比5%-6%的增加.

结论:

  • 通过整合蛋白质结构信息,PHIStruct有效预测菌体与宿主相互作用.
  • 该工具提供了更好的性能,特别是在具有有限序列相似性的场景中.
  • PHIStruct代表了对菌体-宿主特异性的计算预测的重大进步.