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相关概念视频

RNA Structure01:23

RNA Structure

78.7K
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...
78.7K
RNA Structure01:19

RNA Structure

7.1K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
7.1K
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

44.9K
VSEPR Theory for Determination of Electron Pair Geometries
44.9K
Nucleic Acid Structure01:25

Nucleic Acid Structure

8.4K
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...
8.4K
RNA Stability01:53

RNA Stability

35.6K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
35.6K
Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
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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相关实验视频

Updated: Jan 15, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

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DeepRMSF:一种基于深度学习的自动化方法,用于预测RNA结构中的原子级灵活性.

Chenjie Feng1, Xiaowen Sun2, Xintao Song2

  • 1College of Medical Information and Engineering, Ningxia Medical University, No. 1160 Shengli Road, Xingqing District, Yinchuan, Ningxia Province 750004, China.

Briefings in bioinformatics
|January 13, 2026
PubMed
概括
此摘要是机器生成的。

DeepRMSF是一种新的深度学习方法,可以准确地从结构中预测RNA的振动灵活性. 该工具为分析RNA动态的分子动态模拟提供了一个快速,可扩展的替代方案.

关键词:
3D卷积神经网络是一个3D卷积神经网络.预测RNA动态的预测局部灵活性RNA局部灵活性分子动力学模拟模拟

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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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:

  • 了解RNA结构动态对于破译其生物功能至关重要.
  • 从静态结构中预测RNA局部灵活性仍然是一个重大的计算挑战.
  • 现有的方法很难有效地预测RNA的动态特性.

研究的目的:

  • 开发一种基于深度学习的方法,DeepRMSF,用于预测RNA振动灵活性.
  • 为评估RNA局部动态提供一个计算高效的工具.
  • 为了便于大规模分析跨转录组的RNA灵活性.

主要方法:

  • 开发了DeepRMSF,这是一个使用原子级RNA描述的深度学习模型.
  • 从分子动力学 (MD) 模拟中获得的根-平均-平方波动 (RMSF) 训练了模型.
  • 通过严格的交叉验证和独立的测试集,对371个非冗余RNA结构进行了基准DeepRMSF.

主要成果:

  • 在独立的测试组中,DeepRMSF准确地预测了具有高相关性 (PCC ~0.73-0.75) 的RNA振动灵活性.
  • 与传统的MD模拟相比,实现了 >3000倍的速度提升,用于灵活性预测.
  • 对中等大小的RNA (约75个核酸) 证明了强大的推断精度,预测灵活性在8.2秒内.

结论:

  • DeepRMSF提供了一种可扩展和实用的方法,用于转录组范围内的RNA灵活性选.
  • 该方法补充了MD模拟,为分析RNA动态提供了更快的替代方案.
  • 促进对RNA结构-动力学-功能关系的更深入的理解,并有助于计算RNA生物学.