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相关概念视频

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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Conformations of Cyclohexane02:11

Conformations of Cyclohexane

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Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
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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 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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MO Theory and Covalent Bonding02:40

MO Theory and Covalent Bonding

10.3K
The molecular orbital theory describes the distribution of electrons in molecules in a manner similar to the distribution of electrons in atomic orbitals. The region of space in which a valence electron in a molecule is likely to be found is called a molecular orbital. Mathematically, the linear combination of atomic orbitals (LCAO) generates molecular orbitals. Combinations of in-phase atomic orbital wave functions result in regions with a high probability of electron density, while...
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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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相关实验视频

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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分子对接与依赖于调整器的电荷

Huixuan Zhao1, Lei Sun2, Depeng Zhang3

  • 1Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China. huxueping@sdu.edu.cn.

Physical chemistry chemical physics : PCCP
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概括
此摘要是机器生成的。

我们开发了配合器依赖电荷 (MDCC) 的分子对接,提高了蛋白质-联体结合预测的准确性. MDCC取得了60%的成功率,超越了现有方法,并显示了药物发现的前景.

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科学领域:

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

背景情况:

  • 精确预测蛋白质 - 连接体相互作用对于基于结构的药物设计至关重要.
  • 目前的分子对接方法在准确预测结合结构方面面临挑战.
  • 开发先进的计算工具对于克服这些局限性至关重要.

研究的目的:

  • 引入一种新的分子对接方法,即具有符合电荷的分子对接 (MDCC).
  • 与传统方法相比,评估MDCC的对接成功率.
  • 评估MDCC在竞争环境中的表现及其与其他先进技术的潜在整合.

主要方法:

  • 开发MDCC方法,将合规搜索与RESP费用整合在一起.
  • 验证使用PDBbind核心集中的285个蛋白质小分子连接体复合体.
  • 在GPCR Dock 2021竞赛中的申请和与分子动力学模拟的结合.

主要成果:

  • MDCC实现了60%的对接成功率,超过了Glide SP (51.9%) 和Glide XP (52.6%).
  • 对于特定的连接体类型 (大疏水性表面积,原子数或分子量),MDCC的成功率超过90%.
  • 在GPCR Dock 2021竞赛中,MDCC的排名很高 (APJ排名第二,GPR139排名第五).

结论:

  • MDCC在预测蛋白质 - 配体结合结构方面提供了显著的改进.
  • 该方法显示了更高的准确性,特别是对于具有挑战性的连接体类型.
  • MDCC具有实用药物设计的潜力,包括与AlphaFold 2和分子动力学模拟的集成.