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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
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
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

12.9K
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:
12.9K
Complexometric Titration: Ligands00:43

Complexometric Titration: Ligands

961
Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...
961
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

20.8K
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
20.8K
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...
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Updated: Jul 8, 2025

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

Published on: June 20, 2025

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增强带姿势采样用于分子对接.

Patricia Suriana1, Ron O Dror1

  • 1Department of Computer Science, Stanford University.

ArXiv
|December 11, 2023
PubMed
概括
此摘要是机器生成的。

新的姿势采样方法,GLOW (增强型采样与软化vdW潜力) 和IVES (代组合采样),提高了分子对接的准确性. 这些方法增强了候选连接体姿势的生成,以便更好地训练得分功能和虚拟选.

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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
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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.
  • 机器学习 机器学习

背景情况:

  • 深度学习显著增强了分子对接,用于结合姿势预测和虚拟选.
  • 准确的候选姿势生成对于训练得分功能和执行分子对接至关重要.
  • 当前的姿势采样协议往往无法产生近似的姿势,从而限制了得分函数的准确性.

研究的目的:

  • 开发和评估改进的姿势采样协议,用于分子对接.
  • 为了提高连接体结合姿势预测的准确性,特别是对于灵活的结合口袋.
  • 为研究界提供有价值的数据集和开源工具.

主要方法:

  • 引入了两种新的姿势采样协议:GLOW (增强型采样与软化vdW潜力) 和IVES (代组合采样).
  • 使用实验确定和AlphaFold生成的蛋白质结构对拟议的方法进行了基准测试.
  • 产生了大约5000个蛋白质 - 配体交叉对接的候选配体姿势的综合数据集.

主要成果:

  • 与现有的方法相比,GLOW和IVES显著提高了采样准确的连接体结合姿势的可能性.
  • 增强的采样效率对于表现出形状灵活性的结合口袋特别值得注意.
  • 在原生和计算生成的蛋白质结构中,性能改进一致.

结论:

  • 开发的姿势采样协议解决了当前分子对接方法的局限性.
  • GLOW和IVES促进了更准确的评分功能开发和虚拟选.
  • 提供开源实现和数据集,以推进该领域的研究.