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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

12.9K
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...
12.9K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

13.0K
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:
13.0K
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
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
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...
4.8K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

215
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
215

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相关实验视频

Updated: Jul 13, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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通过考虑绑定亲和关系信息,对蛋白质-连接体相互作用进行代基于知识的评分函数.

Xuejun Zhao1, Hao Li1, Keqiong Zhang1

  • 1School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China.

The journal of physical chemistry. B
|October 12, 2023
PubMed
概括
此摘要是机器生成的。

我们通过结合具有约束力的亲和关系数据,改进了ITScore得分功能到ITScoreAff. 这种增强的模型在预测药物设计的蛋白质 - 配体相互作用方面表现出卓越的性能.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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相关实验视频

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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科学领域:

  • 计算化学是一种计算化学.
  • 结构生物学是结构生物学.
  • 药物发现 药物发现

背景情况:

  • 评分功能对于基于结构的药物设计至关重要.
  • 基于知识的评分功能提供了适用性和效率的平衡.
  • 当前基于知识的函数在准确的结合亲和力预测方面遇到了困难.

研究的目的:

  • 通过整合实验性的结合性亲缘关系数据,开发一个改进的基于知识的评分功能,ITScoreAff.
  • 为了提高蛋白质 - 配体相互作用的预测准确度.

主要方法:

  • 通过修改代的基于知识的评分函数 ITScore.ff 开发了 ITScoreAff.
  • 训练有素的ITScoreAff对6216个蛋白质连接体复合物的大型数据集进行了训练,具有结构和亲和数据.
  • 使用CASF-2016基准对其他40个评分函数进行ITScoreAff的评估.

主要成果:

  • 与现有方法相比,ITScoreAff在对接,排名和选功率方面表现出卓越的性能.
  • 在对接功率方面实现了85.3%的成功率,在得分功率方面实现了0.723的相关系数.
  • 在考虑排名中前10%的化合物时,展示了最好的选能力.

结论:

  • 与传统和机器学习分数函数相比,ITScoreAff代表了显著的改进.
  • 结合约束性亲和数据的整合提高了基于知识的评分函数的稳定性和预测能力.
  • ITScoreAff显示了更准确的基于结构的药物设计和虚拟查的前景.