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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

12.8K
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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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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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:
12.9K
Conserved Binding Sites01:49

Conserved Binding Sites

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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

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相关实验视频

Updated: Jun 28, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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AutoDock-SS:用于多元信息化的基于基的虚拟选的AutoDock.

Boyang Ni1, Haoying Wang1, Huda Kadhim Salem Khalaf1

  • 1Institute for Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K.

Journal of chemical information and modeling
|April 16, 2024
PubMed
概括

AutoDock-SS通过调整对接以用于基于联体的虚拟选 (LBVS) 来增强药物领先发现. 这种方法准确地考虑了连接体的灵活性,优于现有的3D LBVS方法.

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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
  • 化学信息学 化学信息学

背景情况:

  • 基于连接体的虚拟查 (LBVS) 对于在蛋白质结构不可用时识别药物线索至关重要.
  • 现有的LBVS方法往往无法充分考虑连接体的结构灵活性,从而限制了它们的有效性.

研究的目的:

  • 介绍AutoDock-SS (相似性搜索),一个新的3D LBVS工作流程,集成基于联体的网格地图和AutoDock-GPU.
  • 通过结合动态形态搜索来解决当前LBVS方法的局限性.

主要方法:

  • 开发了AutoDock-SS,这是一个适用于LBVS的蛋白质-连接体对接的工作流.
  • 集成了基于联体的新型网格地图和AutoDock-GPU.
  • 实现了内置的构造性搜索,用于对连接体构造的动态优化.
  • 支持单个和多个连接体查询模式.

主要成果:

  • 在单一参考模式下,AutoDock-SS在DUD-E数据集上实现了0.775的平均AUROC和25.72的EF1%的平均EF1%.
  • 在DUD-E+的多引用模式下,AutoDock-SS表现出卓越的准确性,平均AUROC为0.843和EF1%的34.59.
  • 在两种测试模式中,超越了替代的3D LBVS方法.

结论:

  • AutoDock-SS 通过将连接体作为形状灵活的处理,显著增强了 LBVS.
  • 该方法准确考虑了连接体形状,药和静电电位.
  • AutoDock-SS扩展了LBVS在药物发现中的功能和潜在应用.