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

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...
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

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...

You might also read

Related Articles

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

Sort by
Same author

dynsight: An open Python platform for simulation and experimental trajectory data analysis.

The Journal of chemical physics·2026
Same author

Monomer exchange dynamics in ureido-pyrimidinone supramolecular polymers <i>via</i> molecular simulations.

Journal of materials chemistry. B·2025
Same author

Observation of shuttling on the one-second timescale in a [10]cycloparaphenylene/C<sub>60</sub> [2]catenane.

Chemical science·2025
Same author

The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior.

ACS central science·2025
Same author

Reciprocity in dynamics of supramolecular biosystems for the clustering of ligands and receptors.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

A Dynamic Silver(I) Nanocluster Holds Together a 3 × 3 Self-Assembled Grid.

Journal of the American Chemical Society·2025

Related Experiment Video

Updated: Jul 1, 2026

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

Unbiased Structure Prediction of Sophisticated Cage Structures.

Andrew Tarzia1,2, Giovanni M Pavan1

  • 1Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.

Angewandte Chemie (International Ed. in English)
|June 30, 2026
PubMed
Summary

This study introduces unbiased cage structure prediction software, cgx, enabling the discovery of novel molecular cages. The method uses minimal models and exploration algorithms, reducing experimental costs and accelerating chemical discovery.

Keywords:
cage compoundscomputational chemistrygraphsminimal modelsstructure prediction

More Related Videos

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

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

Related Experiment Videos

Last Updated: Jul 1, 2026

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

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

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

Area of Science:

  • Computational Chemistry
  • Materials Science
  • Supramolecular Chemistry

Background:

  • Current cage structure prediction methods often rely on known structures, limiting the discovery of novel candidates.
  • Evaluating all potential structural candidates computationally is crucial for designing new materials.

Purpose of the Study:

  • To introduce unbiased structure prediction workflows for novel cage discovery using the cgx software.
  • To enable computational design and evaluation of all structural candidates, reducing reliance on prior experimental data.

Main Methods:

  • Development of unbiased structure prediction workflows within the cgx software.
  • Utilizing exploration algorithms and low-cost minimal models for efficient candidate evaluation.
  • Validating predictions against experimental data using building block types, features, and stoichiometry as inputs.

Main Results:

  • The cgx software successfully predicts cage structures from basic experimental inputs without prior structural knowledge.
  • Demonstrated the ability to predict structures prior to costly experimental commitments.
  • The approach is automated, open-source, and applicable to various model resolutions.

Conclusions:

  • The developed unbiased prediction method facilitates the efficient, automated discovery of novel cage structures.
  • The open-source cgx software and provided documentation with code recipes lower the barrier for chemists to adopt this predictive approach.