Jove
Visualize
联系我们
JoVE
x logofacebook logolinkedin logoyoutube logo
关于 JoVE
概览领导团队博客JoVE 帮助中心
作者
出版流程编辑委员会范围与政策同行评审常见问题投稿
图书馆员
用户评价订阅访问资源图书馆顾问委员会常见问题
研究
JoVE JournalMethods CollectionsJoVE Encyclopedia of Experiments存档
教育
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab Manual教师资源中心教师网站
使用条款与条件
隐私政策
政策

相关概念视频

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

12.8K
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:
12.8K
Molecular Models02:00

Molecular Models

37.8K
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.
37.8K
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...
4.2K

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序
Same author

Phosphate Solvation in Mixed Organic-Aqueous Solutions: Implications for Marble Conservation Treatments.

The journal of physical chemistry. B·2026
Same author

Counterpoise Correction and Charge Embedding as Antidotes for Delocalization Error in Density Functional Many-Body Expansion.

The journal of physical chemistry letters·2025
Same author

Metal-dependant structural families of aminomethylphosphonic acid assemblies differentiated by ion mobility mass spectrometry and density functional theory.

Chemical communications (Cambridge, England)·2025
Same author

Cavity formation energy drives the accumulation of amphiphiles at the air-water interface.

Chemical communications (Cambridge, England)·2025
Same author

Gas Phase Mass- and Mobility-Resolved Structures of Metalated Glyphosate Dimers.

Journal of the American Society for Mass Spectrometry·2025
Same author

Fatty Alcohol Membrane Model for Quantifying and Predicting Amphiphilicity.

Journal of chemical information and modeling·2024

相关实验视频

Updated: May 30, 2025

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.1K

预测二氧化碳无水酶结合亲和力:从QM集群模型的洞察力.

Mackenzie Taylor1, Haedam Mun1, Junming Ho1

  • 1School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia.

The journal of physical chemistry. B
|January 28, 2025
PubMed
概括

开发精确的量子力学 (QM) 集群模型可以改善碳酸酶结合亲和力的预测. 较大的模型增强了预测能力,为混合QM/分子力学 (QM/MM) 方法提供了洞察力.

科学领域:

  • 计算化学是一种计算化学.
  • 生物物理化学 生物物理化学
  • 药物发现 药物发现

背景情况:

  • 碳酸无水酶是各种疾病的关键酶标.
  • 准确预测连接体结合亲和力对于药物开发至关重要.
  • 量子力学 (QM) 方法对于模拟分子相互作用至关重要,但计算成本昂贵.

研究的目的:

  • 开发和验证QM集群模型来预测碳酸无水酶结合亲和力.
  • 在这些模型中评估各种密度函数理论 (DFT) 方法的性能.
  • 为优化QM/MM模拟中的QM区域定义提供见解.

主要方法:

  • 系统地开发各种尺寸的QM集群模型.
  • 使用高级DLPNO-CCSD (T) /CBS计算生成参考结合能量.
  • 对DFT方法的评估,包括r2SCAN-3c和oB97X-3c,与参考数据对比.
  • 质量管理集群模型性能与传统对接方法的比较.

主要成果:

  • 质量管理集群模型的预测准确性随着模型大小的增加而系统地提高.
  • 在较大的模型上,r2SCAN-3c DFT复合方法表现出良好的性能.

更多相关视频

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.2K
Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.2K

相关实验视频

Last Updated: May 30, 2025

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.1K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.2K
Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.2K
  • 质量管理集群模型显示,在预测约束趋势方面,与对接相比有显著的改进.
  • 确定了需要QM治疗的关键相互作用.

    • 结论:

    • 经过验证的QM集群模型提供了一种可靠的方法来预测绑定亲和力趋势.
    • 在较大的集群模型上,r2SCAN-3c提供了一种经济但又准确的方法来预测约束亲和力.
    • 结果为QM/MM模型中的QM区域的战略定义提供了信息,以提高效率和准确性.