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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Discovering protein-DNA binding sequence patterns using association rule mining.

Kwong-Sak Leung1, Ka-Chun Wong, Tak-Ming Chan

  • 1Department of Computer Science & Engineering, The Chinese University of Hong Kong, and Hong Kong Bioinformatics Centre, Shatin, NT, Hong Kong, China.

Nucleic Acids Research
|June 10, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a new framework using association rule mining to uncover associated sequence patterns in protein-DNA interactions. These discovered patterns offer insights into transcription factor and binding site relationships.

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Last Updated: Jun 12, 2026

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Protein-DNA bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are crucial for transcriptional regulation.
  • Existing methods often struggle with the complexity of TF-TFBS interactions, lacking simple rules between amino acids and nucleotides.
  • Investigating associated sequence patterns is essential for understanding functional characteristics of protein-DNA binding.

Purpose of the Study:

  • To develop a framework for discovering associated TF-TFBS binding sequence patterns.
  • To present these patterns in an explicit and interpretable form.
  • To leverage computational power and data mining techniques for biological insights.

Main Methods:

  • Utilized association rule mining, specifically the Apriori algorithm.
  • Applied the framework to the TRANSFAC database for pattern discovery.
  • Evaluated discovered patterns using quantitative measurements and independent verification.

Main Results:

  • Successfully discovered associated sequence patterns between TFs and TFBSs.
  • Patterns were validated through literature, Protein Data Bank, and homology modeling.
  • Evidence suggests the discovered patterns represent real TF-TFBS bindings.

Conclusions:

  • The proposed framework effectively identifies interpretable TF-TFBS binding sequence patterns.
  • These patterns enhance the understanding of TF-TFBS interactions.
  • The findings can drive further research into transcriptional regulation mechanisms.