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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
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.7K
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...
4.7K
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
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
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

47.7K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
47.7K
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

5.7K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
5.7K

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相关实验视频

Updated: May 30, 2025

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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灵活的分子对接的联体条件侧链包装.

Ding Luo1, Xiaoyang Qu2, Dexin Lu1

  • 1State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.

Journal of chemical theory and computation
|January 25, 2025
PubMed
概括

ApoDock通过整合机器学习来增强分子对接,以实现现实的姿势和蛋白质灵活性. 这种新方法提高了准确性,特别是在模拟的蛋白质结构中,推进了药物发现研究.

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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

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

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相关实验视频

Last Updated: May 30, 2025

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

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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

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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:

  • 计算生物学 计算生物学
  • 结构生物信息学 结构生物信息学
  • 药物发现 药物发现 药物发现

背景情况:

  • 分子对接对于理解蛋白质-配体相互作用至关重要.
  • 机器学习 (ML) 的对接方法显示出希望,但与姿势可信性和蛋白质灵活性作斗争.
  • 现有的方法在现实应用中存在局限性.

研究的目的:

  • 为了介绍ApoDock,一个新的模块化对接范式.
  • 在基于ML的对接中解决物理可信性和蛋白质灵活性方面的挑战.
  • 提高分子对接预测的准确性和可靠性.

主要方法:

  • ApoDock将ML驱动的条件侧链包装与传统采样相结合.
  • 它通过考虑蛋白质骨干和带数据来确保物理现实的姿势.
  • 基于混合密度网络的评分函数用于姿势排名.

主要成果:

  • ApoDock 在各种应用程序中展示了竞争力的性能.
  • 它显示使用建模结构 (例如AlphaFold2,ESMFold) 的成功率比最先进的方法高28.5%.
  • 该方法实现了准确的侧链包装,基于物理的姿势采样和可靠的姿势排名.

结论:

  • ApoDock提供了一个强大的解决方案,用于生成物理上可信的蛋白质-连接体对接姿势.
  • 它处理蛋白质灵活性和利用模拟结构的能力使其具有高度价值.
  • ApoDock代表了蛋白质 - 配体结合研究和药物开发的重大进步.