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相关概念视频

Protein and Protein Structures02:15

Protein and Protein Structures

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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....
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Structural Protein Function01:56

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Protein and Protein Structure02:15

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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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Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Conservation of Protein Domains Over Different Proteins02:26

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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.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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S-PLM:通过序列和结构之间的对比学习实现结构感知蛋白质语言模型.

Duolin Wang1, Mahdi Pourmirzaei1, Usman L Abbas2

  • 1Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
|December 12, 2024
PubMed
概括

介绍S-PLM,一种新的3D结构感知蛋白质语言模型 (PLM),它集成了蛋白质序列和结构. 通过提高功能预测和设计能力,S-PLM增强了蛋白质研究.

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相反的学习学习学习.深度学习是一种深度学习.蛋白质功能的预测和预测.蛋白质语言模型蛋白质结构 蛋白质结构

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科学领域:

  • 计算生物学 计算生物学
  • 结构生物信息学 结构生物信息学
  • 机器学习在生物学中的应用

背景情况:

  • 蛋白质对于生物和工程应用至关重要.
  • 蛋白质语言模型 (PLM) 加快了蛋白质功能的确定和设计.
  • 目前的PLM通常缺乏3D结构信息,限制了它们的预测能力.

研究的目的:

  • 开发一个 3D 结构感知 PLM (S-PLM),集成蛋白质序列和结构信息.
  • 提高PLM用于各种生物任务的预测和设计能力.
  • 为各种下游蛋白质预测应用提供可适应的工具.

主要方法:

  • S-PLM采用多视图对比学习来对准蛋白质序列和3D结构表示.
  • 旋转转换器用于嵌入来自AlphaFold预测的蛋白质结构的结构信息.
  • 结构嵌入与ESM2.2的序列嵌入融合在一起.

主要成果:

  • 在蛋白质聚类和分类任务上,S-PLM的表现优于仅序列的PLM.
  • 通过使用序列和结构,S-PLM实现了与最先进的方法可比的性能.
  • 提供了轻量级的调整工具,用于将S-PLM适应特定的预测任务.

结论:

  • S-PLM有效地将3D结构信息集成到蛋白质语言模型中.
  • 该模型在蛋白质功能预测和分类方面表现出卓越的性能.
  • S-PLM为推进蛋白质研究和工程提供了一个有价值的工具.