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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...
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Molecular Models02:00

Molecular Models

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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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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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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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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...
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完全灵活的分子对齐使准确的连接物结构建模成为可能.

Zhihao Wang1, Fan Zhou2, Zechen Wang1

  • 1School of Physics, Shandong University, Jinan, 250100, China.

Journal of chemical information and modeling
|July 29, 2024
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概括

通过使用拓结构信息而不是分子指纹相似性,Z-align 提高了蛋白质-连接体结合的姿势预测. 这种新的方法提高了对齐的精度和准确性,有助于小分子药物设计.

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科学领域:

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

背景情况:

  • 精确的蛋白质连接体结合姿势对于基于结构的药物设计和优化至关重要.
  • 目前基于相似性的分子对齐方法由于分子多样性和必要的修改,精度降低.
  • 预测各种小分子的结合姿势仍然是计算化学的一个重大挑战.

研究的目的:

  • 开发一种新的分子对齐方法,Z-align,可以克服传统基于相似性的方法的局限性.
  • 为了提高蛋白质 - 配体结合的准确性和可靠性,提出预测.
  • 为了促进在小分子药物设计中更有效的优化.

主要方法:

  • Z-align利用拓结构信息作为评估分子相似性的主要标准,减少对分子指纹相似性的依赖.
  • 该方法包括全面和灵活的优化结合长度和角度.
  • 对Z-align的性能进行了评估,并与现有的蛋白质 - 配体对接的方法进行了比较.

主要成果:

  • 与其他方法相比,Z-align的成功率明显更高,特别是在适度的相似程度上.
  • 这种方法即使在处理较大的分子时也能保持高精度.
  • 拓方法提高了对齐精度,解决了基于指纹的方法的局限性.

结论:

  • Z-align 提供了一个更准确,更强大的解决方案,用于预测蛋白质 - 配体结合的姿势.
  • 这一进步可以通过提高优化来加速药物发现过程.
  • Z-align 网络服务器可用于科学界的更广泛使用.