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Related Concept Videos

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 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.
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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.
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Related Experiment Video

Updated: Jun 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein

Krystyna Zakrzewska1, Benjamin Bouvier, Alexis Michon

  • 1Institut de Biologie et Chimie des Protéines, CNRS UMR 5086/Université de Lyon, 7 passage du Vercors, 69367 Lyon, France. k.zakrzewska@ibcp.fr

Physical Chemistry Chemical Physics : PCCP
|February 11, 2010
PubMed
Summary

A new physics-based method, ADAPT, estimates protein-DNA binding energy for all sequences by analyzing fragments. This approach accurately predicts binding for complex systems like nucleosomes, aligning with experimental data.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Related Experiment Videos

Last Updated: Jun 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Understanding sequence-specific protein-DNA interactions is crucial for gene regulation.
  • Existing methods struggle with the combinatorial complexity of analyzing all possible DNA sequences.
  • Proteins binding to the DNA minor groove present unique challenges for computational analysis.

Purpose of the Study:

  • To develop and apply a physics-based computational approach (ADAPT) for analyzing sequence-specific protein-DNA interactions.
  • To estimate binding energies for all potential DNA sequences at the protein-DNA interface.
  • To investigate the role of DNA deformation in protein-DNA recognition.

Main Methods:

  • Utilized the ADAPT (A Divide-and-conquer Approach for Protein-DNA) physics-based method.
  • Employed a divide-and-conquer strategy to break down the protein-DNA interface into smaller fragments.
  • Performed energy minimization using an all-atom representation and a conventional force field for conformational adaptation.
  • Analyzed all possible base sequences for each fragment.

Main Results:

  • The ADAPT method successfully estimated binding energies for three studied protein-DNA complexes.
  • The analysis showed good agreement between computational predictions and experimental data.
  • The approach scales linearly with binding site length, enabling analysis of large complexes like nucleosomes.
  • Significant DNA deformation was observed, but it did not solely dominate sequence recognition.

Conclusions:

  • ADAPT provides an efficient and accurate method for predicting sequence-specific protein-DNA binding.
  • The computational framework allows for detailed analysis of DNA conformational changes upon protein binding.
  • Findings suggest that while DNA deformation is important, sequence-dependent mechanical properties may not always dominate recognition.