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

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.

ATP and Macromolecule Synthesis

ATP and Macromolecule Synthesis

Biological macromolecules are organic compounds, predominantly composed of carbon atoms. The carbon atoms are covalently bonded with hydrogen, oxygen, nitrogen, and other minor elements. There are four major biological macromolecule classes: carbohydrates, lipids, proteins, and nucleic acids.
Most macromolecules are composed of single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers.
Conversion of...

You might also read

Related Articles

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

Sort by

Same author

Enhancing machine learning-based binder design with high-throughput screening: A comparison of mRNA and yeast display technologies.

Protein science : a publication of the Protein Society·2026

Same author

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

bioRxiv : the preprint server for biology·2026

Same author

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

bioRxiv : the preprint server for biology·2026

Same author

Intensity modulation of trichromatic split fluorescent proteins for live cell mapping.

Cell reports methods·2026

Same author

Enhancing Enzymatic Bioconjugation Efficiency via Computer-Based Installation of a Substrate Recruitment Domain.

Bioconjugate chemistry·2026

Same author

Restraining Interproton Angular and Distance Dynamics with KEnRef.

The journal of physical chemistry. B·2026

Search research articles

Related Experiment Video

Updated: Jun 5, 2026

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

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

Andrew Leaver-Fay¹, Michael Tyka, Steven M Lewis

¹Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, USA.

Methods in Enzymology

|December 29, 2010

Summary

The ROSETTA molecular modeling program has been re-architectured into ROSETTA3, enhancing functionality and enabling rapid protocol development. This freely available software facilitates advanced molecular modeling research for the scientific community.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Related Experiment Videos

Last Updated: Jun 5, 2026

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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

Computational Biology
Structural Biology
Biochemistry

Background:

The ROSETTA molecular modeling program underwent a significant re-architecture.
This initiative aimed to generalize and expand its existing functionalities.

Purpose of the Study:

To describe the requirements and design decisions behind the new ROSETTA architecture.
To introduce ROSETTA3, a re-architectured version of the ROSETTA program.
To highlight the capabilities of the new software for molecular modeling tasks.

Main Methods:

Re-architecturing of the ROSETTA molecular modeling program.
Development of easy-to-use interfaces for molecular modeling tools.
Release of the source code as ROSETTA3 for academic use.

Main Results:

The new architecture enables rapid prototyping of novel protocols.
ROSETTA3 offers generalized and expanded functionality for molecular modeling.
The source code has grown significantly, indicating ease of use and adoption.

Conclusions:

The re-architectured ROSETTA3 provides a powerful and accessible platform for molecular modeling.
The software's design facilitates the development and implementation of new modeling protocols.
ROSETTA3 is freely available, promoting advancements in computational and structural biology research.