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Related Concept Videos

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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: Jun 19, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

Discovering multiple realistic TFBS motifs based on a generalized model.

Tak-Ming Chan1, Gang Li, Kwong-Sak Leung

  • 1Department of Computer Science & Engineering, The Chinese University of Hong Kong, Shatin, N, T,, Hong Kong. tmchan@cse.cuhk.edu.hk

BMC Bioinformatics
|October 9, 2009
PubMed
Summary

This study introduces GALF-G, a new algorithm for identifying transcription factor binding sites (TFBSs). GALF-G effectively discovers multiple, potentially overlapping TFBSs with variable widths, improving upon existing methods.

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Related Experiment Videos

Last Updated: Jun 19, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

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Published on: February 7, 2019

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

Published on: July 14, 2015

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Transcription factor binding site (TFBS) identification is crucial for understanding gene regulation.
  • Current de novo motif discovery methods often struggle with variable TFBS widths and identifying multiple, overlapping motifs.

Purpose of the Study:

  • To develop a generalized model that accounts for a range of motif widths, addressing uncertainty.
  • To create a meta-convergence framework for genetic algorithms to discover multiple, overlapping motifs simultaneously.

Main Methods:

  • Proposed a generalized model to evaluate a range of motif widths.
  • Developed a meta-convergence framework for genetic algorithms (GAs).
  • Introduced the GALF-G algorithm, combining GAs with local filtering.

Main Results:

  • GALF-G demonstrated superior performance over state-of-the-art methods on over 970 datasets.
  • The range model improved sensitivity compared to single-width models.
  • Achieved up to 73% higher F-scores than MEME on a liver-specific dataset, identifying novel motifs.

Conclusions:

  • GALF-G is an effective and efficient tool for de novo motif discovery, handling variable widths and multiple overlapping motifs.
  • The algorithm offers improved sensitivity and competitive precision, outperforming existing methods in complex biological datasets.