Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Conserved Binding Sites

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Investigating the Function of C‑Terminal Tails of Human Tubulin Isotypes in the Motility Regulation of Cytoplasmic Dynein.

ACS omega·2026

Same author

Impact of N-Terminal Domain Conformation and Domain Interactions on RfaH Fold Switching.

Proteins·2024

Same author

Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions.

Communications chemistry·2023

Same author

Crowding-induced protein destabilization in the absence of soft attractions.

Biophysical journal·2022

Same author

The C-terminal domain of transcription factor RfaH: Folding, fold switching and energy landscape.

Biopolymers·2021

Same author

Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH.

Proteins·2020

Search research articles

Related Experiment Video

Updated: Mar 7, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Binding Specificity Profiles from Computational Peptide Screening.

Stefan Wallin¹

¹Department of Physics and Physical Oceanography, Memorial University, St. John's, NL, A1B 3X7, Canada. swallin@mun.ca.

Methods in Molecular Biology (Clifton, N.J.)

|February 26, 2017

Summary

This summary is machine-generated.

A novel computational peptide screening method uses Monte Carlo simulations to analyze peptide-binding site specificity. This approach enhances molecular simulations with "mutational" moves, enabling efficient characterization of binding affinities and specificity.

Keywords:

Affinity Binding free energy Generalized-ensemble techniques Monte Carlo simulations PDZ domains Protein–peptide interaction

More Related Videos

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Related Experiment Videos

Last Updated: Mar 7, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Area of Science:

Computational biology
Biophysics
Molecular modeling

Background:

Characterizing peptide-binding site specificity is crucial for understanding biological interactions.
Existing methods may lack the efficiency to systematically screen diverse peptide sequences.
Computational approaches offer a promising avenue for detailed binding site analysis.

Purpose of the Study:

To introduce and validate a novel computational peptide screening method.
To systematically characterize the specificity of a peptide-binding site.
To determine the peptide binding specificity of a PDZ domain from the protein GRIP1.

Main Methods:

Utilizing a Monte Carlo-based, generalized-ensemble algorithm.
Enhancing molecular simulations with "mutational" moves for sequence variability.
Performing reference simulations of unbound states and bound states for free energy calculations.

Main Results:

The method successfully parametrized a linear model of unbound state free energy.
Simulations of the bound state revealed skewed sequence distributions towards higher binding free energies.
Information on relative binding affinities and the molecular basis of specificity was obtained.

Conclusions:

The computational peptide screening method provides a robust framework for analyzing peptide-binding site specificity.
The approach allows for the determination of relative binding affinities and the molecular underpinnings of specificity.
This method can be applied to various biological systems, including protein-protein interactions involving PDZ domains.