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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

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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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Conservation of Protein Domains02:26

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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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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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相关实验视频

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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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深层折叠:通过优化损失函数,改进模板功能和重新优化能量函数来增强蛋白质结构预测.

Jae-Won Lee1,2, Jong-Hyun Won1,2, Seonggwang Jeon1,2

  • 1Department of Computer Science, Hanyang University, Seoul 04763, Korea.

Bioinformatics (Oxford, England)
|November 23, 2023
PubMed
概括

DeepFold通过提高侧链准确性和骨干质量来增强超越AlphaFold2的蛋白质结构预测. 这种开源工具为结构生物学提供了实用价值,在CASP15.5中获得了最高排名.

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科学领域:

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

背景情况:

  • 准确的蛋白质结构预测对于生命科学和工业至关重要.
  • 像AlphaFold2这样的深度神经网络具有先进的预测能力,但详细的准确性,特别是侧链,需要改进.

研究的目的:

  • 为了提高蛋白质结构预测的准确性,专注于侧链和骨干细节.
  • 为了在AlphaFold2的成功基础上进行新的修改和重新优化技术.

主要方法:

  • 修改了AlphaFold2,通过调整侧链扭转角度和对齐点误差的损失函数来修改AlphaFold2.
  • 嵌入损失函数用于侧链信心和二次结构预测.
  • 取代了模板特征生成,采用基于条件随机字段的对齐方法,并采用了与分子力学相结合的构造空间化来重新优化.

主要成果:

  • 在单个蛋白质和域建模的CASP15盲测试中,DeepFold在132组中排名第四.
  • 在骨干准确度方面获得了88.64的GDT-TS中位数,超过了AlphaFold2的85.88.8.
  • 与其他表现出色的小组相比,表现出优越的侧链准确性和Molprobity分数.

结论:

  • 在蛋白质结构预测方面,DeepFold提供了显著的改进,特别是侧链细节和整体准确性.
  • 该工具为结构生物学界提供了实用价值,他们要求高精度的蛋白质模型.
  • 作为开源软件,DeepFold可以使用.