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

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

You might also read

Related Articles

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

Sort by

Same author

Hierarchical organ aging signatures from routine abdominal CT add incremental disease risk stratification beyond blood biomarkers.

medRxiv : the preprint server for health sciences·2026

Same author

Antibacterial and antibiofilm activities of novel bacterial topoisomerase inhibitors against Staphylococcus aureus and other clinically relevant pathogens.

European journal of medicinal chemistry·2026

Same author

Cryo-Electron Microscopy Structural Ensemble Optimization Using Individual Particles.

Journal of chemical theory and computation·2026

Same author

Scale adaptive and robust intrinsic dimension estimation via optimal neighbourhood identification.

Scientific reports·2026

Same author

RPA hyperphosphorylation hinders the resolution of R-loops and G-quadruplex-associated R-loops during RAS-driven senescence.

Nucleic acids research·2026

Same author

Enzymes for Synthesis and Degradation of Bio-Based Polyesters: Automatic In Silico Screening and Experimental Validation.

ChemSusChem·2026

Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Sep 30, 2025

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

Computational Evolution Protocol for Peptide Design.

Rodrigo Ochoa¹, Miguel A Soler², Ivan Gladich^3,4

¹Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin, Colombia.

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

|March 17, 2022

Summary

This summary is machine-generated.

This study introduces PARCE, an open-source computational peptide design tool. It uses molecular dynamics to accurately model peptide-target interactions for developing therapeutics and vaccines.

Keywords:

Affinity optimization Antibody design Consensus scoring functions Evolutionary algorithm In silico antibody maturation Molecular dynamics Peptide design Sensor technology

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

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

Related Experiment Videos

Last Updated: Sep 30, 2025

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

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

Area of Science:

Computational biology
Biochemistry
Drug discovery

Background:

Accurate modeling of peptide-target interactions is crucial for computational peptide design.
Existing methods may not fully capture the molecular details of these interactions.

Purpose of the Study:

To review a computational peptide design protocol utilizing all-atom explicit solvent molecular dynamics.
To introduce the open-source code PARCE, implementing this protocol.
To demonstrate the protocol's application and broad scope through examples.

Main Methods:

Utilizing all-atom explicit solvent molecular dynamics simulations.
Developing and implementing a computational peptide design protocol.
Providing a tutorial for the open-source PARCE code.
Applying the method to design antibody fragments and peptides for various targets.

Main Results:

The developed protocol accurately describes peptide-target interactions at the molecular level.
The protocol is implemented in the open-source PARCE code.
Demonstrated successful application in designing antibody fragments and peptides for diverse targets.

Conclusions:

The PARCE protocol offers a robust approach for computational peptide design.
The method's ability to model molecular interactions enhances the selection of promising peptide candidates.
The open-source nature and demonstrated applications highlight its broad utility in therapeutics, diagnostics, and vaccine development.