RBProkCNN: 深度学习适当的上下文进化信息,以发现 prokaryotes 中的 RNA 结合蛋白质
Upendra Kumar Pradhan1, Sanchita Naha2, Ritwika Das3
1Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
Computational and structural biotechnology journal
|April 25, 2024
概括
我们开发了RBProkCNN,这是一种机器学习模型,可以准确预测 prokaryotic RNA 结合蛋白 (RBP). 这种工具提供了高精度,并优于现有的RBP识别方法.
科学领域:
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- RNA结合蛋白 (RBPs) 对于 prokaryotes 中的转录后调节至关重要.
- 对真核RBPs的研究广泛,但对 prokaryotic RBPs的研究仍然不足.
- 现有的计算方法在识别 prokaryotic RBPs 时缺乏准确性.
研究的目的:
- 开发一种新的,准确的计算模型来预测 prokaryotic RBPs.
- 解决原生生物RBP识别的通用预测方法的局限性.
主要方法:
- 利用了八个浅层学习算法和四个深度学习模型.
- 基于集成的位置特定得分矩阵 (PSSM) 的进化特征.
- 使用卷积神经网络 (CNN) 结合极端梯度增强来进行特征选择.
主要成果:
- 在五次交叉验证中,RBProkCNN实现了98.04%的auROC和98.19%的auPRC.
- 在独立数据集上表现出强的表现,auROC 95.77%和auPRC 95.78%.
- 在预测准确度方面表现优于现有的几种最先进的模型.
结论:
- RBProkCNN是一种非常准确和高效的工具,用于预测 prokaryotic RBP.
- 该模型及其在线预测工具增强了RBP研究的资源.
- 这一进步有助于更深入地了解 prokaryotic 基因调节.
相关概念视频
01:49Conserved Binding Sites
4.2K
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...
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...
4.2K
00:43Bacterial RNA Polymerase
29.5K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
29.5K
01:53Bacterial Transcription
28.1K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.1K
02:24Ribosome 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...
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...
3.5K
01:23Types of RNA
63.6K
Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
63.6K
02:26Conservation of Protein Domains Over Different Proteins
10.8K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.8K