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相关概念视频

Conserved Binding Sites01:49

Conserved Binding Sites

5.2K
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...
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Conserved Binding Sites01:49

Conserved Binding Sites

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Transcription Factors02:16

Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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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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Ligand Binding Sites02:40

Ligand Binding Sites

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Transcription Elongation Factors02:35

Transcription Elongation Factors

14.0K
Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
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Constructing and Visualizing Models using Mime-based Machine-learning Framework
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一个基于DNABERT的深度学习框架,用于预测转录因子结合部位.

Pratik Dutta1, Nimisha Ghosh2, Daniele Santoni3

  • 1Department of Computer Science and Engineering, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India. pratikdutta@soa.ac.in.

Scientific reports
|February 3, 2026
PubMed
概括
此摘要是机器生成的。

我们开发了TFBS-Finder,这是一个用于预测转录因子结合站点 (TFBS) 的深度学习模型. 我们的模型优于现有的方法,增强对基因调节的理解.

关键词:
DNA 序列的 DNA 序列.DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABERT DNABER深度学习 (Deep Learning) 是一种深度学习.转录因子绑定站点

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科学领域:

  • 基因组学就是基因组学.
  • 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:

  • 转录因子 (TFs) 通过与称为转录因子结合位 (TFBSs) 的特定DNA序列结合来调节基因表达.
  • 准确的TFBS预测对于破译基因调节网络和细胞功能至关重要.
  • 现有的TFBS预测深度学习模型提供了改进的空间.

研究的目的:

  • 开发一种先进的深度学习模型,TFBS-Finder,用于准确预测转录因子绑定站点.
  • 利用预先训练的模型和新的注意力机制,从DNA序列中提取增强的特征.

主要方法:

  • TFBS-Finder模型集成了预训练的DNABERT,用于序列嵌入和捕获远程依赖.
  • 它包含卷积神经网络 (CNN),修改卷积区注意模块 (MCBAM) 和注意的多尺度卷积 (MSCA),用于局部特征提取.
  • 该模型在165个ENCODE ChIP-seq数据集上进行了训练和验证.

主要成果:

  • 与现有方法相比,TFBS-Finder在TFBS预测方面表现优越.
  • 废除研究和跨细胞系验证证实了该模型的有效性.
  • 视觉分析为预测结果的解释性提供了洞察力.

结论:

  • 拟议的TFBS-Finder模型在预测转录因子结合站点方面取得了重大进展.
  • 它的架构有效地结合了远程和局部特征提取,以提高准确性.
  • 该模型的可解释性和卓越性能使其成为基因组研究的宝贵工具.