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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
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...
4.2K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

43.3K
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...
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Conservation of Protein Domains02:26

Conservation of Protein Domains

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Atomic Force Microscopy01:08

Atomic Force Microscopy

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Atomic force microscopy (AFM) is a type of scanning probe microscopy that can analyze topographic details of various specimens like ceramics, glass, polymers, and biological samples. AFM offers over 1000 times more resolution than the optical imaging system. Images generated from AFM are three-dimensional surface profiles, offering an advantage over the flat, two-dimensional images from other imaging techniques.
The AFM Probe
The probe is regarded as the heart of any AFM setup and comprises the...
3.3K
Amides to Amines: LiAlH4 Reduction01:20

Amides to Amines: LiAlH4 Reduction

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Amide reduction with strong reducing agents like lithium aluminum hydride proceeds through a nucleophilic acyl substitution to form amines. Primary, secondary, and tertiary amides yield primary, secondary, and tertiary amines, respectively.
Amide reduction requires two equivalents of the reducing agent, acting as a source of hydride ions. As shown in the figure, the reaction is initiated with a nucleophilic attack by the hydride ion at the carbonyl carbon to form a tetrahedral intermediate.
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DPAM-AI:一个由人工智能驱动的AlphaFold模型的域解析器.

Jesse Durham1,2,3, Jing Zhang1,2,3, Richard D Schaeffer3,4

  • 1Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States.

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概括

一个新的AI工具DPAM-AI准确地将来自AlphaFold蛋白质结构数据库 (AFDB) 的蛋白质结构细分为进化领域. 这通过完善域边界和识别多单元域来推进对蛋白质功能的理解.

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科学领域:

  • 结构生物学 结构生物学
  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学

背景情况:

  • 阿尔法折叠蛋白质结构数据库 (AFDB) 提供了2亿个近原子分辨率的蛋白质结构,几乎覆盖了整个蛋白质宇宙.
  • 将蛋白质模型划分为域,并将其进化分类,对于理解蛋白质功能至关重要.

研究的目的:

  • 介绍DPAM-AI,一个基于人工智能的域解析器用于AlphaFold模型.
  • 在广的AFDB数据集中准确地划分和分类蛋白质域.

主要方法:

  • DPAM-AI采用在蛋白质域进化分类 (ECOD) 数据库上训练的卷积神经网络.
  • 它整合了余量间的距离,预测的对齐错误,以及序列/结构对齐.
  • 使用HHsuite和Dali进行相似性搜索以检测以前分类的域名.

主要成果:

  • 与DPAM,Merizo和Chainsaw相比,DPAM-AI在基准集中表现出更好的表现.
  • 应用于AFDB中的Pfam分类蛋白质,DPAM-AI获得了89%家族的代表性3D结构.
  • 发现15%的Pfam域包含多个结构/进化单元和精细的边界超过一半.

结论:

  • DPAM-AI有效地对AFDB中的蛋白质域进行细分,提供了有价值的结构和进化见解.
  • 该工具完善了域边界,并识别了复杂的多单元域,增强了我们对蛋白质结构和功能的理解.