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相关概念视频

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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Calculating Standard Free Energy Changes02:49

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The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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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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One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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相对BAT:通过分离拓方法进行相对约束性自由能计算的自动化工具.

Germano Heinzelmann1, David J Huggins2,3, Michael K Gilson4

  • 1Departamento de Fisica, Universidade Federal de Santa Catarina, Florianopolis 88040-900, Brasil.

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绑定亲和度工具 (BAT.py) 软件现在提供了使用分离拓 (SepTop) 的相对绑定自由能量 (RBFE) 计算. 这种方法通过准确预测各种联体的结合亲和力,降低计算成本,提高了药物发现.

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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:

  • 使用分子动力学 (MD) 的绝对 (ABFE) 和相对结合自由能量 (RBFE) 计算对于成本效益高的早期药物发现至关重要.
  • 现有方法面临的挑战是连接体相似性,封闭的结合点和受体构造变化.

研究的目的:

  • 引入绑定亲和度工具 (BAT.py) 软件的新实现.
  • 将使用分离拓 (SepTop) 的 RBFE 计算纳入自动化工作流.
  • 解决传统ABFE和RBFE方法的局限性.

主要方法:

  • 在BAT.py.py.中为RBFE计算实施了三个不同的热力学路径.
  • 使用AMBER和OpenMM模拟引擎进行分子动力学模拟.
  • 在BRD4 ((2) 基准系统上测试了新的SepTop方法.

主要成果:

  • 评估了SepTop RBFE,ABFE,标准RBFE和实验数据之间的相关性.
  • 评估了与实施的热力学路径相关的计算成本.
  • 证明了SepTop对结构相似性较低或不存在的配体的适用性.

结论:

  • 与SepTop一起的BAT.py软件提供了一种强大而通用的方法,用于进行具有约束力的自由能源计算.
  • SepTop RBFE计算提供了一个有价值的替代方案,克服了药物发现模拟中的常见挑战.
  • 这一进步有可能加快新药候选药物的识别.