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相关概念视频

Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
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...
12.5K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
Ligand Binding Sites02:40

Ligand Binding Sites

12.7K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.7K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

3.7K
3.7K
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 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

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相关实验视频

Updated: Jun 7, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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ProBID-Net:一种用于蛋白质-蛋白质结合接口设计的深度学习模型.

Zhihang Chen1, Menglin Ji1, Jie Qian1

  • 1Department of Medicinal Chemistry, School of Pharmacy, Fudan University 826 Zhangheng Road Shanghai 201203 People's Republic of China wangrx@fudan.edu.cn yfqi@fudan.edu.cn.

Chemical science
|November 21, 2024
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概括

ProBID-Net是一个新的AI工具,通过从已知的蛋白质结构中学习来设计特定的结合蛋白. 它在蛋白质-蛋白质相互作用设计方面表现出色,甚至在没有先前培训数据的情况下预测突变效应.

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科学领域:

  • 计算生物学是一种计算生物学.
  • 蛋白质工程是一种蛋白质工程.
  • 人工智能在药物发现中的作用

背景情况:

  • 蛋白与蛋白相互作用 (PPI) 是生物过程的基础.
  • PPI的计算设计对于生物制药开发至关重要.
  • 当前的人工智能模型经常在设计已知的受体序列的相互作用方面扎.

研究的目的:

  • 引入ProBID-Net,这是一个AI模型,用于基于已知的目标结构设计特定的结合蛋白.
  • 在蛋白质-蛋白质相互作用设计中解决现有的AI模型的局限性.
  • 为了实现生物制药应用的新型结合蛋白的创建.

主要方法:

  • 在ProBID-Net中,他们接受了自然蛋白质-蛋白质复合体和域界面结构的培训.
  • 该模型识别了已知的蛋白质结构的特征,以设计结合蛋白.
  • 使用接口序列恢复率和AlphaFold-Multimer验证来评估性能.

主要成果:

  • ProBID-Net实现了高的接口序列恢复率 (52.7%,43.9%,37.6%),匹配或超过了ProteinMPNN.
  • 由ProBID-Net设计的序列显示了设计目标和预测结构 (AlphaFold-Multimer) 之间的强烈相关性.
  • 该模型展示了在突变时结合亲和力变化的零射击预测能力.

结论:

  • ProBID-Net推进了针对特定蛋白质与蛋白质相互作用的计算蛋白质设计.
  • 该模型为创建新型结合蛋白提供了一个强大的工具.
  • ProBID-Net对生物制药研究和开发有很大的潜力.