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相关概念视频

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.8K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.8K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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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...
3.7K
Protein and Protein Structure02:15

Protein and Protein Structure

79.4K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
79.4K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.1K
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Protein and Protein Structures02:15

Protein and Protein Structures

10.4K
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Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

13.9K
In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered...
13.9K

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相关实验视频

Updated: Jun 24, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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在蛋白质形状探索中对变异自编码器的评估.

Sian Xiao1, Zilin Song1, Hao Tian1

  • 1Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States.

Journal of computational biophysics and chemistry
|June 3, 2024
PubMed
概括

这项研究评估了变异自编码器 (VAE) 进行增强的蛋白质构型采样. VAE可以识别关键蛋白质特征并产生新的构造,改进分子动力学模拟.

科学领域:

  • 计算生物学是一种计算生物学.
  • 生物物理学的生物物理.
  • 结构生物学中的机器学习

背景情况:

  • 分子动力学 (MD) 模拟对于研究蛋白质动力学和功能至关重要.
  • 标准的MD模拟通常很难在实际的时间范围内探索足够的构造空间.
  • 需要改进采样方法来克服这些局限性.

研究的目的:

  • 评估变异自编码器 (VAE) 在帮助探索蛋白质构造景观方面的有效性.
  • 确定VAE是否可以提高蛋白质动态模拟的效率和范围.

主要方法:

  • 将VAE应用于三个不同的建模系统.
  • 分析VAE捕获蛋白质构造的特征特征的能力.
  • 对VAE进行评估,以产生新的,物理上可信的蛋白质构造.

主要成果:

  • VAEs成功地识别了高层次的隐藏信息,使蛋白质构造有所差异.
  • 生成的形状在物理上是可信的,适合直接采样.
  • 与抽象相比,VAE在插值任务中的表现优于抽象.
  • 随着潜在空间尺寸的增加,模型性能和复杂性之间出现了权衡.
关键词:
深度学习是一种深度学习.增强采样 提升采样分子动力学分子动力学蛋白质构成的结构.变量自动编码器变量自动编码器

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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相关实验视频

Last Updated: Jun 24, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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结论:

  • 变异性自编码器显示出作为一种增强蛋白质构造样本的工具的前景.
  • 通过生成相关的形状,VAE可以帮助探索复杂的蛋白质景观.
  • 需要仔细考虑潜伏空间维度,才能在结构生物学中获得最佳的VAE应用.