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相关概念视频

Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
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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Ligand Binding Sites02:40

Ligand Binding Sites

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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 Sites02:40

Ligand Binding Sites

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8.6K
Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
14.4K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

14.8K
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:
14.8K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.5K
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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Updated: Jan 16, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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通过模板引导的组合对接策略来预测蛋白质 - 连接体结构.

Keqiong Zhang1, Qilong Wu1, Sheng-You Huang1

  • 1School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.

Proteins
|October 6, 2025
PubMed
概括
此摘要是机器生成的。

本研究介绍了一个模板引导的集体对接策略,用于CASP16.16中的蛋白质-连接体结构预测. 这种新的方法在38个团队中获得了第4名的排名,证明了它在预测带结合姿势方面的有效性.

关键词:
卡斯普 (CASP) 是一种发现药物的发现.带结合的结合方式分子对接的分子对接.蛋白质联体复合体的复合体基于模板的对接方式

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科学领域:

  • 计算生物学是一种计算生物学.
  • 结构生物学是结构生物学.
  • 药物发现 药物发现

背景情况:

  • 结构预测技术的批判性评估 (CASP) 在CASP15.5中引入了蛋白质连接体复合体结构预测.
  • CASP16将这一类别扩展到制药超级目标,每个超级目标都包含一个具有多个连接体的蛋白质.

研究的目的:

  • 在CASP16.16中开发和评估用于连接体 (LG) 任务的模板导向组合对接策略.
  • 为了利用最近在蛋白质结构预测方面的进展,改进蛋白质 - 连接体复合体建模.

主要方法:

  • 使用MODELER,AlphaFold3和AlphaFold-Multimer生成的结构组合.
  • 在蛋白质数据库 (PDB) 中搜索了使用序列身份,配体相似性和最大共同子结构 (MCS) 的模板.
  • 采用LSalign用于3D连接体对齐,XDock和MDock用于没有模板的预测,以及ITScore用于能源评估.

主要成果:

  • 开发的方法在38个参与CASP16 LG任务的团队中排名第四.
  • 模板引导组合对接策略在蛋白质-连接体结构预测方面被证明是有效的.
  • 成功整合多个结构预测工具和基于模板的方法.

结论:

  • 模板导向组合对接策略是用于蛋白质-连接体复杂结构预测的强有力的方法.
  • 这种方法对药物发现和开发管道有很大的前景.
  • 在CASP16中的表现验证了该战略在推进结构生物学技术方面的潜力.