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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...
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 7, 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

Inferring PDZ domain multi-mutant binding preferences from single-mutant data.

Elena Zaslavsky1, Philip Bradley, Chen Yanover

  • 1Department of Neurology, Mount Sinai School of Medicine, Center for Translational Systems Biology, New York, New York, United States of America.

Plos One
|October 27, 2010
PubMed
Summary
This summary is machine-generated.

Predicting peptide-binding specificity of PDZ domains is crucial for understanding protein networks. A new method accurately predicts multi-mutant binding preferences using generalized single-point mutation effects, winning the DREAM4 challenge.

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Related Experiment Videos

Last Updated: Jun 7, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Published on: January 26, 2024

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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

Published on: July 14, 2015

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Protein interactions are vital for cellular functions.
  • Peptide recognition domains, like PDZ domains, mediate many protein interactions.
  • Predicting binding specificity from primary sequence aids in understanding complex protein networks.

Purpose of the Study:

  • To develop a method for predicting PDZ domain binding specificity.
  • To describe specificity profiles of multi-mutant ERBB2IP-1 domains as position weight matrices.
  • To participate in and win the DREAM4 Peptide Recognition Domain challenge.

Main Methods:

  • Generalized the effects of single point mutations on wild-type domain binding specificities.
  • Combined linear regression for specific ligand positions with position weight matrix averaging for others.
  • Trained the model on publicly available ERBB2IP-1 single-mutant phage display data.

Main Results:

  • Developed a winning method for the DREAM4 Peptide Recognition Domain challenge.
  • Accurately predicted multi-mutant binding preferences of ERBB2IP-1 domains.
  • Demonstrated superior performance over a general PDZ-ligand binding model.

Conclusions:

  • The developed method effectively predicts PDZ domain binding specificity.
  • Training on domain-specific data significantly improves prediction accuracy.
  • This approach advances the understanding of protein-protein interactions mediated by PDZ domains.