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相关概念视频

RNA Structure01:23

RNA Structure

71.4K
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...
71.4K
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.1K
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...
6.1K
Improving Translational Accuracy02:07

Improving Translational Accuracy

9.9K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
9.9K
RNA-seq03:21

RNA-seq

9.9K
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...
9.9K
Conserved Binding Sites01:49

Conserved 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...
4.2K
Nucleic Acids02:43

Nucleic Acids

44.0K
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,...
44.0K

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相关实验视频

Updated: Jun 21, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.4K

线性Alifold:对RNA对齐的线性时间共识结构预测.

Apoorv Malik1, Liang Zhang1, Milan Gautam1

  • 1School of EECS, Oregon State University, Corvallis, OR 97330, USA.

Journal of molecular biology
|July 6, 2024
PubMed
概括
此摘要是机器生成的。

我们开发了LinearAlifold,这是一种快速的RNA结构预测工具,在大型基因组数据集中显著优于RNAalifold. 这种新方法通过快速分析保存的RNA结构来加速病毒诊断和治疗开发.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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A Protocol for Computer-Based Protein Structure and Function Prediction
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相关实验视频

Last Updated: Jun 21, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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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.
  • 基因组学就是基因组学.

背景情况:

  • 从同源序列中预测保存的RNA结构有助于识别病毒诊断和治疗中至关重要的功能元素.
  • 由于立方时间复杂性,RNAalifold等现有工具与大型数据集作斗争,限制了它们对长RNA序列的应用.

研究的目的:

  • 开发一种更快,更准确的方法来预测共识RNA二次结构.
  • 克服现有工具分析大量RNA序列的计算局限性.

主要方法:

  • 基于LinearFold的新算法LinearAlifold实现了关于序列长度和序列数量的线性时间复杂性.
  • 该工具使用400个SARS-CoV-2和相关基因组的数据集对RNAalifold进行了评估,比较了预测准确度和速度.

主要成果:

  • 与RNAalifold相比,LinearAlifold表现出相当大的加快速度 (约为36倍),在0.7小时内完成分析,而在一天内完成分析.
  • 来自LinearAlifold的预测显示,与已知的结构相比,其准确性更高,并且与SARS-CoV-2的实验数据的相关性比RNAalifold.
  • 该工具支持多种能源模型和预测模式,在不到一个小时内处理数百种SARS-CoV变体.

结论:

  • 线性Alifold为预测共识RNA结构提供了一个计算效率高和准确的解决方案,特别是在大型基因组研究中.
  • 这一进步对加速病毒诊断,治疗和理解RNA基因组组织的研究具有重大意义.