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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...
5.0K
Affinity and Avidity01:41

Affinity and Avidity

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Overview
38.5K
Antibody Structure01:10

Antibody Structure

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Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
65.3K
Ligand Binding Sites02:40

Ligand Binding Sites

14.9K
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...
14.9K
Antibody Structure and Classes01:25

Antibody Structure and Classes

8.2K
Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
8.2K
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

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相关实验视频

Updated: Jan 15, 2026

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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通过原子灵活性增强抗体-抗原相互作用预测.

Sara Joubbi1,2, Alessio Micheli1, Paolo Milazzo1

  • 1Department of Computer Science, University of Pisa, Pisa, Italy.

PLoS computational biology
|October 13, 2025
PubMed
概括
此摘要是机器生成的。

预测局部距离差异测试 (pLDDT) 得分可以模拟抗体灵活性,以改善抗原结合预测. 这种方法增强了抗体-抗原相互作用模型,对于开发针对HIV和SARS-CoV-2等病原体的治疗方法至关重要.

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Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques
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Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques
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科学领域:

  • 免疫学和计算生物学
  • 蛋白质结构和动态 蛋白质结构和动态

背景情况:

  • 抗体是疫苗和治疗药物必不可少的关键免疫成分.
  • 模拟抗体-抗原相互作用是复杂的,因为抗体的灵活性和动态结合.
  • 深度学习已经推进了蛋白质结构的预测,但与抗体-抗原动态斗争.

研究的目的:

  • 研究使用预测的局部距离差异测试 (pLDDT) 分数来建模抗体灵活性.
  • 增强抗体-抗原 (Ab-Ag) 相互作用的计算建模.
  • 改进抗体的工程,以提高对可变病原体的亲和力和范围.

主要方法:

  • 使用基于指纹的方法,将pLDDT得分作为残留灵活性指标.
  • 研究了灵活性对抗体特异性任务和Ab-Ag相互作用建模的影响.
  • 使用接收器操作特征曲线下的面积 (AUC-ROC) 评估模型性能.

主要成果:

  • 通过pLDDT得分将灵活性纳入,提高了Ab-Ag相互作用模型的预测精度4%,达到92%的AUC-ROC.
  • 在帕拉托普预测中展示了最先进的性能.
  • 在抗体建模中,pLDDT得分被证明是对抗体建模中的形状灵活性有价值的代表.

结论:

  • 考虑到形状灵活性对于准确的抗体-抗原相互作用建模至关重要.
  • pLDDT评分提供了一种实用的方法来表示和优化抗体灵活性.
  • 这种方法对对抗HIV和SARS-CoV-2等高度可变的病原体的抗体进行工程具有重大前景.