相关实验视频
Updated: Jul 22, 2025

13:42
RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
31.6K
GCNfold:一种新的轻量级模型,用于RNA二次结构预测的有效提取器
Enbin Yang1, Hao Zhang2, Zinan Zang1
1College of Computer Science and Technology, Jilin University, Changchun, 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130012, China.
Computers in biology and medicine
|July 24, 2023
概括
新的深度学习模型GCNfold精确地有效地预测RNA二级结构. 它以更少的参数和更快的速度实现了高精度,超过了较大的模型.
科学领域:
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
- 分子生物学分子生物学
背景情况:
- 预测RNA的二级结构对于理解RNA的功能和三级结构至关重要.
- 目前的深度学习模型达到>70%的准确性,但需要高的培训成本和缓慢的预测效率.
- 需要准确,高效,并且在计算上便宜的RNA结构预测方法.
研究的目的:
- 开发一种新的深度学习模型,GCNfold,用于准确高效的RNA二次结构预测.
- 在准确性,参数数量和推断速度方面调查GCNfold的性能.
- 为更广泛的研究使用提供GCNfold的开源实现.
主要方法:
- GCNfold使用三个特征提取器:用于结构信息的图形卷积网络 (GCN),用于结构序列融合的变压器编码器,以及用于长距离依赖提取的UNet.
- 该模型使用GCN集成了结构图案,如茎和循环.
- 变压器编码器将结构信息嵌入到序列表示中,而UNet捕获远程交互.
主要成果:
- GCNfold实现了超过80%的准确性,在性能上超越了现有的模型.
- 该模型展示了一个小的参数数量和快速推断速度.
- GCNfold-Small变异在90毫秒内预测RNA的二次结构,平均准确率接近90%.
结论:
- GCNfold为RNA二次结构预测提供了一个高度准确和计算高效的解决方案.
- 该模型的效率和准确性使其适用于大规模的基因组研究.
- GCNfold代表了计算RNA生物学的重大进步,代码可在GitHub上找到.
相关概念视频
Protein Folding Quality Check in the RER
3.8K
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...
3.8K
RNA Structure
71.6K
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...
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...
71.6K
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...
DNA Structure
DNA...
6.2K
RNA-seq
10.1K
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...
10.1K
Protein Folding
118.5K
Overview
118.5K
Extraction: Advanced Methods
488
Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is...
488

