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

Amino acids03:42

Amino acids

103.7K
Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...
103.7K
What are Proteins?01:28

What are Proteins?

19.5K
Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino acids. However, polypeptides have a molecular weight of fewer than 10,000 daltons, while proteins have greater molecular weight.  Polypeptides with less than 20 amino acids are called oligopeptides or simply peptides. Interactions among the constituent amino acid side chains of proteins help them fold into a stable 3-dimensional...
19.5K
Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

1.0K
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
1.0K

You might also read

Related Articles

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

Sort by
Same author

Drug Repurposing: Conversion of the Peripherally Restricted HIV Protease Inhibitor Amprenavir to Potent, Selective, and CNS-Penetrant Agonists for the Cannabinoid Receptor 2.

Journal of medicinal chemistry·2026
Same author

Pregnancy- and Abortion-Related Mortality in the US, 2018-2021.

JAMA network open·2026
Same author

A generalizable deep learning framework for structure-based protein-ligand affinity ranking.

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

Identification of asporin as a HER3 ligand exposes a therapeutic vulnerability in prostate cancer.

JCI insight·2025
Same author

FakeRotLib: Expedient Noncanonical Amino Acid Parametrization in Rosetta.

Journal of chemical information and modeling·2025
Same author

FakeRotLib: expedient non-canonical amino acid parameterization in Rosetta.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Jan 10, 2026

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

816

Parameterizing non-canonical amino acids for cyclic peptide simulations.

N Kithmini Wijesiri1, Benjamin P Brown1

  • 1Department of Pharmacology, Center for AI in Protein Dynamics, Vanderbilt University, Nashville, TN, United States.

Methods in Enzymology
|November 20, 2025
PubMed
Summary

This guide simplifies creating custom parameters for non-canonical amino acids (ncAAs) in biomolecular modeling. It enables efficient use of ncAAs in cyclic peptide design and molecular dynamics simulations.

Keywords:
AMBERCyclic peptidesMolecular dynamicsNon-canonical amino acidsParameterizationRosettaUnnatural amino acids

More Related Videos

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System
11:47

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

16.4K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.5K

Related Experiment Videos

Last Updated: Jan 10, 2026

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

816
Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System
11:47

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

16.4K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.5K

Area of Science:

  • Biomolecular modeling
  • Computational chemistry
  • Peptide design

Background:

  • Non-canonical amino acids (ncAAs) expand chemical space for biomolecular design, especially for cyclic peptides requiring precise interactions.
  • Physics-driven methods are preferred for ncAAs due to generalizable energy functions, but parameter creation is challenging.
  • Existing parameters are limited to canonical amino acids, necessitating custom definitions for ncAAs.

Purpose of the Study:

  • To provide a comprehensive guide for building custom non-canonical amino acid (ncAA) parameters.
  • To facilitate the use of ncAAs in biomolecular modeling and molecular dynamics (MD) simulations.
  • To enable efficient generation of robust ncAA parameters for Rosetta and AMBER.

Main Methods:

  • Developed a step-by-step protocol for creating ncAA residue definitions.
  • Provided sample scripts for parameter generation compatible with Rosetta and AMBER.
  • Included validation checkpoints and representative outputs for quality control.

Main Results:

  • Successfully generated custom ncAA parameters for use in Rosetta and AMBER.
  • Demonstrated the protocol's effectiveness for cyclic peptide modeling.
  • Provided a reproducible workflow for ncAA parameterization.

Conclusions:

  • The developed guide and resources streamline the process of incorporating ncAAs into biomolecular modeling and simulations.
  • Novice and expert users can efficiently generate custom ncAA parameters for advanced peptide design.
  • This work lowers the barrier to entry for utilizing the expanded chemical space offered by ncAAs.