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

Search research articles

Related Experiment Video

Updated: May 21, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Pep2MARS: Automated Cyclic Peptide Parameterization for Molecular Dynamics and Compound Design.

Junhao Li¹, Yue Qian¹

¹Viva Biotech (Shanghai) Limited, 735 Ziping Road, Pudong New District, Shanghai 201318, P. R. China.

Journal of Chemical Information and Modeling

|May 19, 2026

Summary

This study introduces an automated workflow to streamline the creation of parameter files for cyclic peptide molecular dynamics (MD) simulations. This new method simplifies complex setups for macrocyclic peptides, making them easier to study.

Related Concept Videos

You might also read

Related Articles

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

Sort by

Same author

EnsembleCycPerm: Interpretable Modeling of Cyclic Peptide Permeability through Solvent-Dependent Conformational Ensembles.

Journal of chemical information and modeling·2026

Same author

Unveiling the Activation Mechanism of Glucagon-Like Peptide-1 Receptor by an Ago-Allosteric Modulator via Molecular Dynamics Simulations.

Journal of chemical information and modeling·2026

Same author

TMBIM6/BI-1 is an intracellular environmental regulator that induces paraptosis in cancer via ROS and Calcium-activated ERAD II pathways.

Oncogene·2024

Same author

Breaking the Gender Imbalance: Female Presence in the Computational Chemistry Group at Viva Biotech.

Journal of chemical information and modeling·2024

Same author

Exploring the Interactions between two Ligands, UCB-J and UCB-F, and Synaptic Vesicle Glycoprotein 2 Isoforms.

ACS chemical neuroscience·2024

Same author

Adaptive lambda schemes for efficient relative binding free energy calculation.

Journal of computational chemistry·2023

Area of Science:

Computational chemistry
Biophysics
Drug discovery

Background:

Cyclic peptides are promising drug candidates for targeting difficult proteins.
Molecular dynamics (MD) simulations are crucial for studying peptide behavior.
Generating parameter files for cyclic peptides with non-standard amino acids is challenging and labor-intensive.

Purpose of the Study:

To develop an automated workflow for generating topology and force field parameter files for cyclic peptide systems.
To simplify and expedite the setup process for macrocyclic peptide MD simulations.

Main Methods:

An automated workflow was developed for processing partial charges and force field parameters of non-standard amino acids.
The workflow was tested on cyclic peptides with mono- to tetra-cyclization in both bound and unbound states.

More Related Videos

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

Related Experiment Videos

Last Updated: May 21, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

Parameter files were validated for consistency across different molecular dynamics engines.

Main Results:

The automated workflow successfully generated valid parameter files for various cyclic peptide systems.
Simulation results using the automated workflow were comparable to those from manual setups and different MD engines.
The process demonstrated rigor and transferability across different cyclization patterns.

Conclusions:

The developed tool chain significantly streamlines the setup of macrocyclic peptide MD simulations.
This automation maintains accuracy and allows for consistent application across diverse peptide structures and simulation platforms.
The workflow enhances the utility of MD simulations in cyclic peptide drug discovery.