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相关概念视频

Conserved Binding Sites01:49

Conserved Binding Sites

5.3K
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...
5.3K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

15.5K
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:
15.5K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.9K
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...
5.9K
Ligand Binding Sites02:40

Ligand Binding Sites

15.6K
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...
15.6K
Affinity Chromatography01:03

Affinity Chromatography

3.3K
Affinity chromatography is a powerful technique extensively utilized for separating and purifying specific biomolecules from complex mixtures. It capitalizes on the highly selective binding between an analyte and its counterpart, such as antibody-antigen interactions. The counterpart is immobilized on the stationary phase, forming an affinity column. The stationary phase typically consists of solid support, such as agarose or porous glass beads, immobilizing the affinity ligand. The mobile...
3.3K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

762
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
762

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相关实验视频

Updated: Mar 15, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

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使用分离拓方法对基于碎片的化合物进行高效的绑定亲和度估计.

Ana-Maria Caldaruse1, Hannah M Baumann2, David L Mobley1

  • 1School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.

Journal of chemical information and modeling
|March 13, 2026
PubMed
概括
此摘要是机器生成的。

基于碎片的药物发现 (FBDD) 从准确的结合亲和力预测中受益. 分离拓 (SepTop) 方法在建模片段转换和优化药物线索方面显示出前景.

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Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
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Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates
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相关实验视频

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Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
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Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay

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Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates
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科学领域:

  • 计算化学计算化学
  • 药物发现 药物发现 药物发现
  • 生物物理学的生物物理.

背景情况:

  • 基于碎片的药物发现 (FBDD) 对早期药物开发至关重要.
  • 预测碎片和类型的结合亲和关系,由于弱相互作用和结构多样性,会带来计算挑战.
  • 现有的自由能源方法往往没有针对FBDD的特定需求进行优化.

研究的目的:

  • 评估分离拓 (SepTop) 方法用于模拟药物发现中的基于片段的转换.
  • 评估SepTop在预测碎片合并和链接的绑定亲缘关系方面的准确性.
  • 确定SepTop适合在早期药物开发中进行片段优化.

主要方法:

  • 使用已建立的FBDD数据集进行回顾性分析 (Cyclophilin D,SARS-CoV-2 Macrodomain 1).
  • 分离拓的应用 (SepTop) 计算方法.
  • 对碎片和类化合物进行具有约束力的自由能量计算的验证.

主要成果:

  • 该SepTop方法准确地恢复了实验性的结合亲和关系.
  • 在碎片和类化合物中观察到良好的预测准确性.
  • SepTop在模拟碎片合并和链接转换方面表现出有效性.

结论:

  • SepTop是FBDD中片段优化的合适方法.
  • SepTop可以将绑定自由能量计算的应用扩展到更早的药物发现阶段.
  • 这种方法增强了开发新疗法的计算策略.