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相关概念视频

RNA Structure01:19

RNA Structure

4.8K
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...
4.8K
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...
6.2K
RNA-seq03:21

RNA-seq

10.0K
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...
10.0K
Nucleic acids02:43

Nucleic acids

163.4K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
163.4K
Three-Domain System of Life01:21

Three-Domain System of Life

33
Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...
33
The DNA Helix01:07

The DNA Helix

20.8K
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
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相关实验视频

Updated: Jul 13, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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使用欧几里德神经网络从核酸序列预测3DRNA结构.

Congzhou M Sha1, Jian Wang2, Nikolay V Dokholyan3

  • 1Department of Engineering Science and Mechanics, Penn State University, State College, Pennsylvania; Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania.

Biophysical journal
|October 15, 2023
PubMed
概括

我们开发了一种快速卷积神经网络,用于3DRNA结构预测,在RNA中达到100个核酸的高度精度. 这种方法比传统的分子动力学模拟速度快数百万倍.

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

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相关实验视频

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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科学领域:

  • 结构生物学是结构生物学.
  • 计算生物学是一种计算生物学.
  • 生物物理学的生物物理.

背景情况:

  • 准确的三维 (3D) RNA结构预测至关重要,但由于RNA的尺寸,灵活性和有限的实验数据,这是一个挑战.
  • 与DNA不同,RNA的较少受约束的基配对导致了许多可能的稳定结构,使预测变得复杂.
  • 现有的方法,如分子动力学,是计算密集且缓慢的.

研究的目的:

  • 开发一种快速而准确的计算方法,用于从核酸序列预测3DRNA结构.
  • 利用机器学习,特别是卷积神经网络,克服现有预测技术的局限性.

主要方法:

  • 一个卷积神经网络 (CNN) 旨在预测RNA残留物之间的对距离.
  • CNN利用欧几里德距离矩阵的平滑参数化进行预测.
  • 一个粗的机器学习输出被转换为一个全原子模型,使用受约束的离散分子动力学.

主要成果:

  • 美国有线电视新闻网 (CNN) 对长度高达100个核酸的RNA分子进行了高准确度的预测.
  • 预测速度比传统的分子动力学方法快了数量级 (10~7倍).
  • 该管道成功地从核酸序列直接生成了全原子RNA模型.

结论:

  • 拟议的基于CNN的管道为3DRNA结构预测提供了更快,更准确的方法.
  • 尽管速度很快,但该方法的性能受限于用于训练的实验确定RNA结构的稀缺性,类似于分子动力学.
  • 这项工作代表了计算机RNA结构建模的实质性进展,为更高效的分析铺平了道路.