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相关概念视频

Nucleic Acid Structure01:25

Nucleic Acid Structure

6.2K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
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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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Predicting Molecular Geometry02:27

Predicting Molecular Geometry

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VSEPR Theory for Determination of Electron Pair Geometries
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Molecular Shapes01:18

Molecular Shapes

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Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
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Molecular Models02:00

Molecular Models

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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相关实验视频

Updated: Jul 13, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

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通过对语言模型预测结构的几何图形学习准确识别核酸结合点.

Yidong Song1, Qianmu Yuan1, Huiying Zhao1

  • 1Key Laboratory of Machine Intelligence and Advanced Computing of MOE, School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China.

Briefings in bioinformatics
|October 12, 2023
PubMed
概括

使用快速,可预测的结构,GLMSite准确地预测蛋白质上的DNA和RNA结合点. 这种方法克服了现有工具的局限性,有助于发现蛋白质功能.

关键词:
绑定站点 绑定站点几何图形学习学习几何图形学习核酸是核酸中的一种.预先训练的语言模型语言模型.

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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:

  • 预测核酸-蛋白相互作用对于理解生物过程至关重要,但仍然具有挑战性.
  • 目前的基于序列的方法缺乏结构上下文,而传统的基于结构的方法需要实验确定蛋白质结构.
  • 像AlphaFold2这样的高性能结构预测工具是计算密集型的,限制了全基因组应用.

研究的目的:

  • 开发一种准确和有效的方法来识别蛋白质上的DNA和RNA结合点.
  • 为了利用ESMFold的快速蛋白质结构预测,用于结合部位预测.
  • 为了使核酸与蛋白质相互作用的大规模分析,并促进蛋白质功能发现.

主要方法:

  • 开发了GLMSite,一种使用ESMFold预测蛋白质结构的几何图形学习方法.
  • 构建的蛋白质结构图,其残留物作为节点,空间邻居作为边缘.
  • 使用ProtTrans语言模型增强节点表示,并训练了一个几何向量感知子网络.
  • 整合几何嵌入到一个共同的网络中,以学习共享的绑定特征,然后使用完全连接的层进行预测.

主要成果:

  • GLMSite能够准确地识别蛋白质上的DNA和RNA结合部位.
  • 该方法超越了现有的基于序列的预测工具.
  • GLMSite的性能与传统的基于结构的方法相美.
  • 预测对于推断核酸结合蛋白和发现蛋白质功能是有价值的.

结论:

  • 使用预测的蛋白质结构,GLMSite提供了一种高效和准确的方法来预测核酸结合部位.
  • 该方法解决了当前基于序列和结构的技术的局限性.
  • GLMSite对促进蛋白质功能发现和大规模基因组研究具有重大潜力.