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相关概念视频

Allosteric Regulation01:08

Allosteric Regulation

Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
Allosteric Regulation01:08

Allosteric Regulation

Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...

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Updated: Jun 28, 2026

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

精细调节的diffdock-l用于化激酶对接.

Eric Chen1, Justin Green2, Yingkai Zhang3,2

  • 1Department of Chemistry, New York University, New York, New York 10003, United States.

Journal of chemical information and modeling
|March 4, 2026
PubMed
概括
此摘要是机器生成的。

这项研究介绍了AlloSet,这是一个新的数据集,用于训练人工智能模型,以准确预测全激酶抑制剂结合姿势. 微调的DiffDock-L-Allo模型显示了对挑战全结合剂的改进性能.

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Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
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Published on: June 23, 2026

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科学领域:

  • 计算化学计算化学
  • 结构生物学 结构生物学
  • 药物发现 药物发现 药物发现

背景情况:

  • 阿洛斯特基纳酶抑制剂提供了选择性,但对当前的AI对接模型构成挑战.
  • 现有的模型往往错误地预测ATP结合部位内的全联体结合模式.

研究的目的:

  • 策划一个全面的数据集 (AlloSet) 用于评估和改进人工智能驱动的全激酶抑制剂的姿势预测.
  • 微调DiffDock-L模型以提高预测全结合模式的准确性.

主要方法:

  • 策划的AlloSet,一个带有绑定模式注释的全基因组数据集.
  • 微调了DiffDock-L模型,使用了增加脱落率和分子动力学超采样等策略.
  • 评估了对全和正配体的性能,与AlphaFold3和Boltz-2进行了比较.

主要成果:

  • 微调的DiffDock-L-Allo模型显著改善了III/IV型全结合剂的姿势恢复.
  • 保持了对orthosteric (ATP站点) 配体的性能.
  • 有针对性的再培训重塑了模型的采样分布,以更好地预测低数据绑定模式.

结论:

  • 微调基于扩散的模型与专用数据集,如AlloSet对于准确的全性激酶抑制剂的姿势预测至关重要.
  • 这种方法为推进基于激酶结构的药物设计中的AI提供了实际指导,特别是对于具有挑战性的结合模式.