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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

12.7K
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...
12.7K
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

134
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...
134
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

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相关实验视频

Updated: Jun 8, 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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DeepLigType:使用深度学习模型预测蛋白质连接结位的连接类型.

Orhun Vural, Leon Jololian, Lurong Pan

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    |November 7, 2024
    PubMed
    概括
    此摘要是机器生成的。

    DeepLigType使用深度学习模型准确地预测蛋白质-连接体结合部位类型. 这种计算方法通过对抗剂,激动剂,激活剂,抑制剂等的结合位点进行分类来帮助药物发现.

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    Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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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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    Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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    Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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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

    Published on: November 3, 2011

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    科学领域:

    • 计算生物学是一种计算生物学.
    • 药物发现 药物发现
    • 生物信息学是一种生物信息学.

    背景情况:

    • 蛋白质 - 配体结合部位分析对于早期药物发现至关重要.
    • 预测连接体类型可以改善药物设计决策.
    • 实验方法是用来描述结合部位的常见方法.

    研究的目的:

    • 开发一种计算方法,DeepLigType,用于预测蛋白质-连接体结合部位的类型.
    • 将结合部位分为五类:对抗剂,激动剂,激活剂,抑制剂等.
    • 利用深度学习来提高预测准确度.

    主要方法:

    • 使用Fpocket识别蛋白质 - 配体结合位点.
    • 采用了一个卷积块注意模块 (CBAM) 与ResNet (CBAM-ResNet) 深度学习模型.
    • 从PDBbind和scPDB创建了一个新的数据集,LigType5,用于培训和测试.

    主要成果:

    • 该CBAM-ResNet模型在预测带类型方面实现了74.30%的准确性.
    • 该模型在新型测试数据集上获得了0.83的曲线下面面积 (AUC).
    • 成功将蛋白质 - 配体结合部位分为五个不同的功能类别.

    结论:

    • DeepLigType提供了一个强大的计算替代方案,用于绑定站点分析的实验方法.
    • 开发的深度学习架构在预测连接体类型方面显示出显著的潜力.
    • 准确的连接体类型预测可以加速和完善药物发现过程.