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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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.
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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.
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Types of RNA01:20

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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 regulating 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.
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Cooperative Binding of Transcription Regulators02:13

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Protein Networks02:26

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Nucleic Acid Structure01:25

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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.
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Updated: Jul 24, 2025

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers.

Ke Yan1, Jiawei Feng1, Jing Huang2,3,4

  • 1School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China.

Briefings in Bioinformatics
|July 5, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces iDRPro-SC, a novel method for accurately predicting nucleic acid-binding protein types using sequence information. The approach considers subfunctions, outperforming existing methods in disease research.

Keywords:
ensemble learningnucleic acid-binding proteins identificationsubfunction classifiers

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Nucleic acid-binding proteins regulate gene expression and are crucial in human disease pathogenesis.
  • Current sequence-based methods for identifying these proteins overlook crucial subfunctional differences.
  • Accurate identification of nucleic acid-binding proteins is vital for advancing disease research.

Purpose of the Study:

  • To develop an improved method for predicting the types of nucleic acid-binding proteins using sequence information.
  • To address the limitations of existing methods by considering the internal functional diversity of these proteins.

Main Methods:

  • Proposed iDRPro-SC, a novel prediction method utilizing sequence information.
  • Incorporated subfunctional differences of nucleic acid-binding proteins into a comprehensive dataset.
  • Employed ensemble learning techniques for protein characterization and prediction.

Main Results:

  • iDRPro-SC demonstrated superior prediction performance on the test dataset.
  • The method outperformed existing nucleic acid-binding protein prediction techniques.
  • A publicly accessible web server (http://bliulab.net/iDRPro-SC) was established.

Conclusions:

  • iDRPro-SC offers a more accurate approach to predicting nucleic acid-binding protein types by accounting for subfunctional variations.
  • This advancement has significant implications for disease research and understanding gene regulation.
  • The developed web server facilitates broader application and accessibility of the prediction tool.