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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 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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相关实验视频

Updated: May 23, 2025

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

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一个大规模对接和实验结果的数据库.

Brendan W Hall1, Tia A Tummino1, Khanh Tang1

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

bioRxiv : the preprint server for biology
|March 10, 2025
PubMed
概括
此摘要是机器生成的。

一个新的数据库共享数十亿个分子对接结果,使机器学习能够用于药物发现. 虽然模型随着更多数据的增加而得到改善,但高对接得分的预测并不能保证找到有效的药物候选者.

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Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
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Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

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Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease
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Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease

Published on: May 10, 2024

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相关实验视频

Last Updated: May 23, 2025

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

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Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

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Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease
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Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease

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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
  • 机器学习 机器学习

背景情况:

  • 在过去的六年中,可访问的化合物显著增加,增强了分子对接技术.
  • 分享对接活动结果对于对比机器学习 (ML) 和化学太空探索方法至关重要.

研究的目的:

  • 创建一个公开可访问的网站,提供大规模的分子对接活动数据.
  • 为11个目标提供63亿个对接分子的姿势,分数和体外结果.
  • 为了促进基准测试和探索不断扩大的化学空间.

主要方法:

  • 开发了一个网站 (lsd.docking.org) 来托管对接活动数据.
  • 在11个目标上对接了63亿个分子.
  • 在实验中测试了3729种化合物.
  • 训练有素的ML模型预测对接得分并识别得分最高的分子.

主要成果:

  • 在较大的数据集上训练的模型显示性能有所改善.
  • ML预测和对接分数之间的高相关性并不总是导致有效带的成功丰富.
  • 即使是来自对接的顶级分子也不能保证实验成功,这突出了当前预测模型的局限性.

结论:

  • 新的数据库支持ML模型培训和化学空间探索.
  • 预测模型需要进一步改进,因为高的对接分数并不总是转化为实验验证.
  • 开放共享大规模的对接数据对于推进药物发现方法至关重要.