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相关概念视频

Protein Organization01:24

Protein Organization

6.2K
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....
6.2K
Protein and Protein Structure02:15

Protein and Protein Structure

78.5K
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...
78.5K
Leaky Scanning02:28

Leaky Scanning

5.1K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.1K
Protein and Protein Structures02:15

Protein and Protein Structures

10.3K
10.3K
Termination of Translation01:44

Termination of Translation

25.0K
The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
25.0K
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

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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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蛋白质序列和结构的双语语言模型.

Michael Heinzinger1, Konstantin Weissenow1, Joaquin Gomez Sanchez1

  • 1School of Computation, Information, and Technology (CIT), Department of Informatics, Bioinformatics & Computational Biology, TUM (Technical University of Munich), 85748 Garching/Munich, Germany.

NAR genomics and bioinformatics
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概括
此摘要是机器生成的。

我们开发了 ProstT5,一种新型的蛋白质语言模型 (pLM),集成了 3D 结构和 1D 序列数据. 这种方法增强了与结构相关的预测,并加速了蛋白质结构数据库的分析.

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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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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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科学领域:

  • 计算生物学是一种计算生物学.
  • 结构生物信息学 结构生物信息学
  • 在基因组学中的机器学习.

背景情况:

  • 蛋白质语言模型 (pLMs) 已经推进了蛋白质序列的分析.
  • AlphaFold2彻底改变了蛋白质结构预测,产生了大量的3D结构数据.
  • 了解蛋白质需要整合它们的1D序列和3D结构信息.

研究的目的:

  • 开发一个统一的模型,同时分析蛋白质序列和结构数据.
  • 利用pLM来建模蛋白质作为序列和3D机器的双重性质.
  • 创建一种新的方法,用于在3D结构表示和氨基酸序列之间进行翻译.

主要方法:

  • 将蛋白质结构编码为符号序列,使用Foldseek.ek的3Di字母表.
  • 在AlphaFoldDB的非冗余数据集上微调现有的pLM (ProtT5).
  • 开发蛋白质"结构序列"T5 (ProstT5) 模型用于联合结构序列分析.

主要成果:

  • ProstT5在与结构相关的预测任务上表现得更好.
  • 在导出3D结构表示 (3Di) 中实现了三次数加速.
  • 建立了将plm与大规模蛋白质结构数据集成的概念验证.

结论:

  • ProstT5有效地模拟了蛋白质序列和结构,弥合了pLMs和结构生物信息学之间的差距.
  • 这种方法对未来的应用至关重要,它可以在大型元基因组数据库中进行结构敏感的搜索.
  • ProstT5通过将结构预测集成到基于序列的分析中,为后AlphaFold2时代开辟了新的研究途径.