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相关概念视频

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

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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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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Valence Bond Theory and Hybridized Orbitals02:38

Valence Bond Theory and Hybridized Orbitals

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According to valence bond theory, a covalent bond results when: (1) an orbital on one atom overlaps an orbital on a second atom, and (2) the single electrons in each orbital combine to form an electron pair. The strength of a covalent bond depends on the extent of overlap of the orbitals involved. Maximum overlap is possible when the orbitals overlap on a direct line between the two nuclei.
A σ bond (single bond in a Lewis structure) is a covalent bond in which the electron density is...
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Problem-Solving: Tuning of a Guitar String01:04

Problem-Solving: Tuning of a Guitar String

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In the case of stringed instruments like the guitar, the elastic property that determines the speed of the sound produced is its linear mass density or the mass per unit length. This is simply called the linear density. If the string's linear density is constant along the string, then the linear density is simply the total mass divided by the total length.
The string's wave speed can be regulated by varying the linear density. Tension is the other property that determines the speed of...
434
Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

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The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
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相关实验视频

Updated: Jul 7, 2025

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

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将潜在函数调整为主机-客户端绑定数据.

Jeffry Setiadi1, Simon Boothroyd2,3, David R Slochower4

  • 1Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9255 Pharmacy Lane, La Jolla, California 92093, United States.

Journal of chemical theory and computation
|December 26, 2023
PubMed
概括
此摘要是机器生成的。

这项研究引入了一种使用宿主-客人系统来训练力场的新方法,以更准确地预测蛋白质-连接体结合亲缘关系. 优化的参数显示了更好的结合预测和更快的计算,有助于药物发现.

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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions
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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

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Probe Type II Band Alignment in One-Dimensional Van Der Waals Heterostructures Using First-Principles Calculations
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Last Updated: Jul 7, 2025

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions
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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
  • 分子建模分子建模

背景情况:

  • 在药物发现中,基于物理学的方法对于预测蛋白质-连接体结合亲缘关系至关重要.
  • 这些方法的准确性在很大程度上取决于用于模拟的潜在函数质量.
  • 实验性的结合亲缘关系尚未被广泛用于训练这些潜在的功能.

研究的目的:

  • 扩展开放力场评估器框架,用于计算主机-客户结合的自由能量.
  • 策划实验性主机-客户绑定数据,用于训练潜在的功能.
  • 使用主机-客户数据,为OBC2隐性溶剂模型优化概括的Born (GB) 腔半径.

主要方法:

  • 系统计算主机-客户结合的自由能量及其梯度.
  • 策划126个宿主-客人综合体的实验性结合自由能量.
  • 针对36个主机-客户系统,优化OBC2 GB模型空腔半径.

主要成果:

  • 主机-客户系统的训练和测试集的精度大幅提高.
  • 优化半径从宿主-客人到蛋白质-连接体系统的证明可转移性.
  • 确定了精确的结合亲和度和具有优化半径的无水化能量之间的权衡.

结论:

  • 主机-客机系统可以有效地训练可转移的潜在函数,用于蛋白质-连接体结合亲缘关系的预测.
  • 开发的基础设施使得计算药物发现的新应用成为可能.
  • 隐式溶剂模型为具有约束力的自由能量计算提供了显著的加速,这表明虚拟选的实用性.