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Updated: Jan 9, 2026

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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.

Journal of chemical information and modeling
|December 1, 2025
PubMed
概括

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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Conserved Binding Sites01:49

Conserved Binding Sites

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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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 Strength

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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