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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
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-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

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相关实验视频

Updated: Jul 17, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

318

使用CB-Dock2进行蛋白质-连接体盲对接.

Yang Liu1, Yang Cao2

  • 1Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.

Methods in molecular biology (Clifton, N.J.)
|September 7, 2023
PubMed
概括
此摘要是机器生成的。

CB-Dock2是一个新的,准确和用户友好的盲人对接服务器,用于蛋白质 - 连接体相互作用. 它增强了结合部位的识别和构造预测,有助于制药和生物研究.

关键词:
绑定站点预测预测盲目的对接 盲目的对接在CB-Dock2中使用.蛋白质连接和对接网络服务器的Web服务器.

更多相关视频

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

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相关实验视频

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

318
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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科学领域:

  • 生物信息学是一种生物信息学.
  • 化学信息学 化学信息学
  • 计算生物学 计算生物学

背景情况:

  • 蛋白质-连接体盲对接对于药物发现和理解生物过程至关重要.
  • 准确识别结合部位和预测连接体位置是关键的挑战.

研究的目的:

  • 介绍一下CB-Dock2,这是一款全新的盲点对接服务器.
  • 提供使用CB-Dock2.2的指南.
  • 评估用CB-Dock2.2进行蛋白质-合物盲对接的性能.

主要方法:

  • 为CB-Dock开发基于知识的对接引擎2.2.
  • 实现自动化,交互式 Web 接口,以方便用户.
  • 对于盲目对接的性能评估的案例研究.

主要成果:

  • 与现有方法相比,CB-Dock2在结合部位识别和构成预测方面表现出卓越的准确性.
  • 服务器高度自动化,高效和用户友好.
  • 案例研究验证了该工具的有效性.

结论:

  • CB-Dock2是科学界的一个强大且易于使用的工具.
  • 它在制药和生物研究中推进了蛋白质-连接体相互作用研究.
  • 服务器有助于高效的药物发现和生物机制探索.