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相关概念视频

Protein Organization01:24

Protein Organization

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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
Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Protein Folding01:22

Protein Folding

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Overview
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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...
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Protein and Protein Structure02:15

Protein and Protein Structure

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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...
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Protein and Protein Structures02:15

Protein and Protein Structures

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相关实验视频

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Prop3D:一个灵活的,基于Python的机器学习平台,具有蛋白质结构性质和生物物理数据.

Eli J Draizen1,2, John Readey3, Cameron Mura4,5

  • 1Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. edraizen@gmail.com.

BMC bioinformatics
|January 4, 2024
PubMed
概括

Prop3D是一个新的平台,用于创建和共享机器学习 (ML) 的特色蛋白质域数据集. 它提供了Prop3D-20sf数据集,帮助可重复的ML管道开发,同时防止数据泄露.

关键词:
深度学习是一种深度学习.机器学习是机器学习.庞大的并行工作流程.蛋白质结构 蛋白质结构结构生物信息学 结构生物信息学

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科学领域:

  • 结构生物信息学 结构生物信息学
  • 计算生物学 计算生物学
  • 机器学习 机器学习

背景情况:

  • 机器学习 (ML),特别是深度学习,正在通过揭示生物分子数据中的复杂关系来推进结构生物信息学.
  • 高质量,可访问的数据集对于ML至关重要,但其创建具有挑战性,特别是对于复杂的3D蛋白质结构.
  • 可重复的培训和测试数据集对于在结构生物信息学中可靠的ML模型开发至关重要.

研究的目的:

  • 介绍Prop3D,一个创建,共享和重复使用特色蛋白质域库的平台.
  • 提供来自CATH的Prop3D-20sf数据集,用于机器学习应用.
  • 促进在结构生物信息学中开发可靠和可重复的ML管道.

主要方法:

  • 开发了Prop3D框架,用于使用高度可扩展数据服务 (HSDS) 创建系统和可重复的数据集.
  • 特色蛋白质域具有不同的生物物理和进化性质,从原子细节到残留水平的保护.
  • 在云和HPC资源上部署了Prop3D框架,用于可扩展的数据生成.

主要成果:

  • 通过Prop3D,可以创建和共享具有丰富功能集的蛋白质域库.
  • 现在可以使用Prop3D-20sf数据集,其中包含来自20个CATH家族的特色蛋白质域.
  • 数据集可以通过公共HSDS实例访问,并通过Python包装器与流行的ML框架兼容.

结论:

  • 通过HSDS,Prop3D提供了一个可定制的工作流,用于通过HSDS在云平台上生成可扩展的数据集.
  • 该Prop3D-20sf数据集加速了ML管道的开发,并确保了可重复性.
  • 在Prop3D-20sf中数据集的构建解决了来自蛋白质进化关系的数据泄露问题.