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

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Protein Organization

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 Folding

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...

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

You might also read

Related Articles

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

Sort by

Same author

ProtAff: Protein Binding Affinity Prediction via LoRA-Finetuned ESM-2.

bioRxiv : the preprint server for biology·2026

Same author

Deep learning based design of buried hydrogen bond networks with HBDesigner.

bioRxiv : the preprint server for biology·2026

Same author

mRNA delivery of a class 1/4 SARS-CoV-2 neutralizing antibody protects against diverse sarbecoviruses in a lethal mouse challenge model.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Predictions from deep learning propose substantial protein-carbohydrate interplay.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

De novo masking domains that gate TNF-family ligand assembly and activity.

bioRxiv : the preprint server for biology·2026

Same author

Deep mining of the human antibody repertoire identifies frequent and genetically diverse CDRH3 topologies targetable by vaccination.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Visualizing Cell Structures with Minecraft.

Biophysicist (Rockville, Md.)·2025

Same journal

Using Histologic Image Analysis to Understand Biophysical Regulations of Epithelial Cell Morphology.

Biophysicist (Rockville, Md.)·2024

Same journal

A Torsion-Based Rheometer for Measuring Viscoelastic Material Properties.

Biophysicist (Rockville, Md.)·2023

Same journal

Adapting Undergraduate Research to Remote Work to Increase Engagement.

Biophysicist (Rockville, Md.)·2023

Same journal

Dynamical Models of Chemical Exchange in Nuclear Magnetic Resonance Spectroscopy.

Biophysicist (Rockville, Md.)·2023

Same journal

Reflections on undergraduate research mentoring.

Biophysicist (Rockville, Md.)·2022

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 4, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

Kathy H Le¹, Jared Adolf-Bryfogle², Jason C Klima^3,4,5

¹T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States.

Biophysicist (Rockville, Md.)

|February 7, 2022

Summary

This summary is machine-generated.

This study introduces interactive Jupyter Notebook modules for learning biomolecular structure and design using PyRosetta. These freely available resources offer a self-paced, multimedia approach for diverse learners in computational biophysics.

More Related Videos

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

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

Published on: July 25, 2013

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Related Experiment Videos

Last Updated: Oct 4, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

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

Published on: July 25, 2013

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Area of Science:

Computational biophysics
Structural biology
Bioinformatics education

Background:

Biomolecular structure dictates function, making computational prediction and design crucial.
Teaching computational biophysics presents challenges due to diverse student backgrounds and resource levels.
Interactive, self-paced learning materials can effectively engage a broad range of students.

Purpose of the Study:

To develop a hands-on educational strategy for biomolecular structure and design.
To create accessible, interactive learning modules for computational biophysics.
To facilitate the use of PyRosetta for scientific research.

Main Methods:

Developed sixteen workshop-style modules using PyRosetta, a Python library for Rosetta software.
Implemented modules as Jupyter Notebooks executable in Google Colaboratory for web-based access.
Integrated multimedia elements like images, molecular visualization movies, and interactive coding exercises.

Main Results:

Created a comprehensive set of educational modules covering fundamental and applied topics in biomolecular structure and design.
Enabled self-paced, active learning through interactive digital content accessible via a web browser.
Provided free access to all materials, promoting broader adoption of PyRosetta in research.

Conclusions:

The developed PyRosetta modules offer an effective, multimodal approach to teaching biomolecular structure and design.
This educational strategy enhances accessibility for students from various disciplines and resource levels.
The freely available resources aim to empower researchers, particularly those in smaller labs, to utilize PyRosetta.