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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

12.8K
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...
12.8K
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 and Linkage00:49

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
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

12.9K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.9K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

7.9K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
7.9K
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

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相关实验视频

Updated: Jul 4, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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动态绑定:通过深度等价生成模型预测连接体特异性蛋白-连接体复合结构.

Wei Lu1, Jixian Zhang2, Weifeng Huang3

  • 1Galixir Technologies, 200100, Shanghai, China. luwei0917@gmail.com.

Nature communications
|February 5, 2024
PubMed
概括

一种新的深度学习方法DynamicBind准确地预测蛋白质结构,并通过建模蛋白质动态来识别药物标. 这推动了对具有挑战性的目标的计算药物发现.

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

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相关实验视频

Last Updated: Jul 4, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
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科学领域:

  • 计算生物学是一种计算生物学.
  • 结构生物学是结构生物学.
  • 药物发现 药物发现

背景情况:

  • 预测静态蛋白质结构已经进步,但蛋白质动态对于功能和药物发现至关重要.
  • 传统的对接方法将蛋白质视为刚性,限制了它们在蛋白质 - 连接体相互作用中的准确性.
  • 分子动力学模拟对于捕捉蛋白质构造变化而言,在计算上很昂贵.

研究的目的:

  • 介绍DynamicBind,这是一个深度学习方法,用于建模蛋白质动力学,并改进蛋白质-连接体相互作用预测.
  • 开发一种有效地探索蛋白质构造格局的方法,而无需大量采样.
  • 为了提高对接和虚拟选的准确性,用于药物发现.

主要方法:

  • 开发了DynamicBind,一种使用等价几何扩散网络的深度学习方法.
  • 构建了一个光滑的能量景观,以促进蛋白质平衡状态之间的过渡.
  • 验证的DynamicBind对接和虚拟选基准,与现有方法进行比较.

主要成果:

  • 通过DynamicBind,可以从未结合的结构中准确地恢复连接体特定的蛋白质构造.
  • 该方法在对接和虚拟选任务中展示了最先进的性能.
  • DynamicBind有效地处理大型蛋白质构造变化,并识别新目标中的神秘口袋.

结论:

  • DynamicBind提供了一种计算效率高的方法来建模蛋白质动力学和预测相互作用.
  • 该方法显示了加速治疗前所未有的目标治疗药物的开发的巨大潜力.
  • 通过解决蛋白质灵活性问题,DynamicBind扩大了计算药物发现的能力.