对RNA结构的几何深度学习
Raphael J L Townshend1, Stephan Eismann1,1,2, Andrew M Watkins3
1Department of Computer Science, Stanford University, Stanford, CA, USA.
概括
我们开发了一种机器学习方法来预测RNA结构, 这种方法使用最少的数据准确地建模复杂的分子结构,推进药物发现和结构生物学.
科学领域:
- 结构生物学
- 计算化学
- 机器学习
背景情况:
- 三维RNA结构对于生物功能和药物发现至关重要.
- 通过计算预测这些复杂的结构仍然是一个重大挑战.
研究的目的:
- 为准确的RNA结构预测开发一种机器学习方法.
- 在深度学习模型中克服数据限制的评分函数.
主要方法:
- 引入了使用原子坐标作为输入的机器学习方法.
- 在没有RNA特定假设的情况下开发了原子旋转等差得分器 (ARES).
- 在已知18个RNA结构的有限数据集上训练模型.
主要成果:
- 该ARES评分功能显著优于之前的RNA结构预测方法.
- 这种方法在全社区的盲目预测挑战中取得了最佳表现.
- 通过小型数据集进行有效的学习,这与标准深度神经网络相比是一个关键优势.
结论:
- 开发的机器学习方法可以准确预测RNA结构.
- ARES为药物发现和结构生物学研究提供了强大的工具.
- 该方法的适用性扩展到RNA结构以外的各种科学领域.
相关概念视频
Nucleic Acid Structure
7.6K
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...
DNA Structure
DNA...
7.6K
RNA-seq
10.6K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.6K
RNA Stability
34.2K
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...
34.2K
Nucleic Acids
47.0K
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,...
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,...
47.0K
Nucleic acids
179.2K
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,...
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,...
179.2K
Experimental RNAi
6.5K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.5K


