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相关概念视频

RNA Structure01:23

RNA Structure

71.4K
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
71.4K
Nucleic Acid Structure01:25

Nucleic Acid Structure

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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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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome Profiling02:24

Ribosome Profiling

3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Analyzing and Building Nucleic Acid Structures with 3DNA
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RNA3DB:一个结构不相似的数据集,用于训练和对比深度学习模型,用于RNA结构预测.

Marcell Szikszai1, Marcin Magnus1, Siddhant Sanghi2

  • 1Department of Molecular and Cellular Biology, Harvard University, Cambridge, 02138, MA, USA.

Journal of molecular biology
|March 29, 2024
PubMed
概括

由于有限的数据和重叠的数据集,RNA结构预测面临着挑战. RNA3DB提供了一个非冗余的数据集和强大的分割方法,用于可靠的深度学习模型基准测试.

关键词:
RNA结构同质性是RNA的结构同质性.预测RNA结构 预测RNA结构结构性RNA的数据集.对RNA深度学习方法的培训.

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科学领域:

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

背景情况:

  • 像AlphaFold这样的深度学习模型已经推进了蛋白质结构预测,增加了对RNA结构预测的兴趣.
  • 由于实验数据稀少,与蛋白质相比,RNA结构预测具有挑战性,结构多样性有限.
  • 现有的RNA结构预测文献经常报告由于具有显著结构重叠的训练和测试集而导致膨胀的性能.

研究的目的:

  • 引入RNA3DB,这是一个新的数据集,用于训练和对比深度学习模型,用于RNA结构预测.
  • 通过提供非冗余,结构不同的RNA3D链来解决现有数据集的局限性.
  • 为了促进可复制和可定制的数据集分割,用于结构性RNA研究.

主要方法:

  • RNA3DB是从蛋白质数据库 (PDB) 构建的,根据序列和结构将RNA3D链分组为不同的非冗余组件.
  • 开发了一种强大的方法来划分培训,验证和测试集,确保集之间的结构不相似性.
  • 提供了RNA3DB组件的特定70/30列车/测试分割,并将定期更新.

主要成果:

  • RNA3DB数据集和方法允许创建不同的培训,验证和测试集,减轻性能膨胀.
  • 非冗余的分组确保任何分割都保证了结构和顺序上不同的集合.
  • 提供的数据集和源代码有助于对RNA结构预测模型进行可重复的基准测试.

结论:

  • RNA3DB为开发和评估用于RNA结构预测的深度学习模型提供了宝贵的资源.
  • 数据集的设计解决了RNA结构预测的关键挑战,促进了更可靠的模型评估.
  • RNA3DB的方法和工具支持可再生计算生物学研究的进步.