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相关概念视频

Protein Folding01:25

Protein Folding

10.9K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
10.9K
Protein Folding01:22

Protein Folding

125.8K
Overview
125.8K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

5.0K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
5.0K
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
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

46.7K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
46.7K
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

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A Protocol for Computer-Based Protein Structure and Function Prediction
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使用FoldBench进行基准测试,预测全原子生物分子结构.

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  • 1Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.

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一个新的基准,FoldBench,揭示了深度学习模型与多样化的生物分子复杂预测斗争. AlphaFold 3显示出有希望的结果,但在配体对接和抗体-抗原相互作用方面仍然存在挑战.

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科学领域:

  • 计算生物学 计算生物学
  • 结构生物学 结构生物学
  • 生物物理学的生物物理.

背景情况:

  • 对生物分子复杂结构的准确预测对于理解生物过程和设计治疗方法至关重要.
  • 深度学习模型具有先进的生物分子结构预测,包括蛋白质,核酸,连接体和离子.
  • 现有的基准缺乏全面性,阻碍了对模型性能和通用性的严格评估.

研究的目的:

  • 介绍FoldBench,一个广泛的基准数据集,用于评估生物分子复杂结构预测模型.
  • 在各种预测任务中评估当前深度学习模型的性能和通用性.
  • 确定预测各种生物分子相互作用的关键挑战和局限性.

主要方法:

  • 开发了FoldBench,一个包含9个不同的预测任务中的1522个生物组件的数据集.
  • 在FoldBench上评估了多个深度学习模型,分析了不同交互类型的性能.
  • 研究了对训练集相似性和分子多样性等因素的性能依赖.

主要成果:

  • 随着对训练数据的联结体相似性降低,联结体对接的准确性降低,反映了蛋白质与蛋白质相互作用的趋势.
  • 抗体-抗原预测仍然非常具有挑战性,目前的方法失败率超过50%.
  • 与其他评估模型相比,AlphaFold 3在大多数预测任务中表现出卓越的准确性.

结论:

  • 折叠板为严格评估生物分子复杂预测模型提供了一个至关重要的资源.
  • 取得了重大进展,但局限性仍然存在,特别是在预测新型联体相互作用和抗体-抗原复合体方面.
  • 未来的模型开发应该专注于提高概括性和解决特定具有挑战性的交互类型.