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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

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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...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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:
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Ligand Binding and Linkage00:49

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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...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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PGBind:用于蛋白质 - 连接物对接的口袋引导的明确注意力学习.

Ao Shen1,2, Mingzhi Yuan1,2, Yingfan Ma1,2

  • 1Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China.

Briefings in bioinformatics
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概括
此摘要是机器生成的。

这项研究介绍了一种口袋引导的策略,以改善盲目的蛋白质-联结体对接的深度学习. 这种方法增强了蛋白质的特性,导致药物发现中的预测明显更好.

关键词:
人工智能用于科学科学.发现药物的发现.蛋白联盟盲目对接蛋白

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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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科学领域:

  • 计算生物学 计算生物学
  • 药物发现 药物发现 药物发现
  • 结构生物信息学 结构生物信息学

背景情况:

  • 盲目的蛋白质 - 配体对接对于药物发现至关重要,可以在没有先前的口袋知识的情况下预测相互作用.
  • 目前用于盲目对接的深度学习方法具有次优蛋白质特征,忽视了口袋区域差异.

研究的目的:

  • 提出一种口袋导向的策略,以增强盲目蛋白质-连接体对接的蛋白质特征.
  • 提高基于深度学习的盲目对接方法的准确性和效率.

主要方法:

  • 开发了一个plug-and-play模块来估计蛋白质上潜在的口袋区域.
  • 实施了口袋引导的注意力机制,以改进蛋白质特征提取.
  • 集成该模块与现有的深度学习模型,如EquiBind和FABind.

主要成果:

  • 口袋导向模块显著提高了EquiBind和FABind的盲点对接性能.
  • 与FABind的集成实现了盲蛋白 - 连接对接的最新性能.
  • 该方法通过增强蛋白质特征,有效地引导连接物到潜在的对接点.

结论:

  • 拟议的口袋引导策略为基于深度学习的盲目蛋白质-连接体对接提供了重大进展.
  • 这种方法增强了蛋白质特征表示,导致更高的预测准确性.
  • 该方法有望通过提高对接预测的可靠性来加速药物发现.