Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

4.5K
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...
4.5K
Protein-protein Interfaces02:04

Protein-protein Interfaces

13.9K
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...
13.9K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

57.2K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
57.2K
Ligand Binding Sites02:40

Ligand Binding Sites

13.8K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
13.8K
Protein Organization01:24

Protein Organization

7.7K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
7.7K
Protein Folding01:25

Protein Folding

9.3K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
9.3K

You might also read

Related Articles

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

Sort by
Same author

PEP-EDIT: a web server for the 3D generation and interactive editing of complex peptides.

Nucleic acids research·2026
Same author

Simulated Solute Tempering 2: An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events.

Journal of chemical theory and computation·2025
Same author

Ligand-Induced Biased Activation of GPCRs: Recent Advances and New Directions from In Silico Approaches.

Molecules (Basel, Switzerland)·2025
Same author

Is the Future of Materials Amorphous? Challenges and Opportunities in Simulations of Amorphous Materials.

ACS physical chemistry Au·2025
Same author

Diffusion mechanisms for spinel ferrite NiFe2O4 by using kinetic activation-relaxation technique.

The Journal of chemical physics·2024
Same author

Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization.

Journal of chemical information and modeling·2023

Related Experiment Video

Updated: Sep 30, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

2.0K

A Generalized Attraction-Repulsion Potential and Revisited Fragment Library Improves PEP-FOLD Peptide Structure

Vincent Binette1, Normand Mousseau1, Pierre Tuffery2

  • 1Départment de Physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada.

Journal of Chemical Theory and Computation
|March 17, 2022
PubMed
Summary
This summary is machine-generated.

Enhanced PEP-FOLD improves small peptide structure prediction accuracy. New generalized force fields and fragment libraries offer better model ranking and insights into folding dynamics.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.2K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.0K

Related Experiment Videos

Last Updated: Sep 30, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

2.0K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.2K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.0K

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Accurate peptide structure prediction is crucial for understanding molecular function and interactions.
  • The PEP-FOLD technique has been a popular method for simplified peptide structure prediction.
  • Previous versions used a fixed-radius van der Waals formulation for coarse-grained energy assessment.

Purpose of the Study:

  • To present improvements to the PEP-FOLD technique for small peptide structure prediction.
  • To explore a generalized force field formulation for more effective coarse-grained representation.
  • To enhance model accuracy and ranking for challenging peptide targets.

Main Methods:

  • Utilized a predetermined structural alphabet and sequential reconstruction algorithm.
  • Implemented a generalized force field with variable interaction parameters and side-chain radii.
  • Updated the fragment library and compared performance against APPTest, RaptorX, and AlphaFold2.

Main Results:

  • The enhanced PEP-FOLD shows significant improvements in model ranking and accuracy for previously problematic targets.
  • New predictions are superior to APPTest and RaptorX, particularly for small beta-targets.
  • The approach provides additional insights into folded structures, complementing AlphaFold2's precision.

Conclusions:

  • The revised structural library and coarse-grained potential enhance peptide structure prediction.
  • This improved method offers a basis for deeper understanding of peptide folding, flexibility, and dynamics.
  • PEP-FOLD's unique approach provides valuable insights beyond purely data-driven AI methods.