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相关概念视频

Protein Organization01:24

Protein Organization

6.5K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.5K
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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Antibody Structure and Classes01:25

Antibody Structure and Classes

953
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.
953
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...
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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使用AlphaFold2进行分子对接的增强抗体-抗原结构预测.

Francis Gaudreault1, Christopher R Corbeil1, Traian Sulea2,3

  • 1Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada.

Scientific reports
|September 13, 2023
PubMed
概括

这项研究通过结合基于物理的对接与AlphaFold2 (AF2) rescoring来增强抗体-抗原复杂结构预测. 新的AF2复合分数显著提高了预测这些关键生物医学结构的准确性.

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科学领域:

  • 结构生物学 结构生物学
  • 计算生物学 计算生物学
  • 免疫学 免疫学 免疫学

背景情况:

  • 预测抗体-抗原复杂结构对于生物医学研究至关重要,但具有挑战性.
  • 虽然AlphaFold2 (AF2) 在蛋白质结构预测方面表现出色,但其对抗体-抗原复合体的应用因缺乏共同进化数据而受到限制.

研究的目的:

  • 为了提高抗体-抗原复杂结构的预测准确度.
  • 开发和验证一种使用AF2.2进行蛋白质-蛋白质对接的新型rescoring方法.

主要方法:

  • 使用基于物理的蛋白质对接生成潜在抗体-抗原复杂结构的诱集.
  • 应用AF2来改进结构,并使用规范化的pLDDT和pTMscore指标计算一个复合得分.
  • 评估AF2复合分数来分类正确和不正确的对接姿势,并提高成功率.

主要成果:

  • AF2复合分数有效地恢复了对接姿势,改善了与原生结构类似的结构的分类.
  • 观察到预测成功率的显著提高,特别是对正确模型的早期丰富.
  • 质量中等的对接模型,不一定是对接方法排名最高的,从AF2 rescoring中受益最多.

结论:

  • 提出的基于AF2的复合方法大大提高了抗体-抗原不结合的对接性能.
  • 这种方法可以实现前所未有的性能水平,而不需要新的方法或校准.
  • 这些发现为推进抗体-抗原复杂结构的预测提供了一个有希望的策略.