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

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Peptide Bonds

Peptide Bonds

A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...

You might also read

Related Articles

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

Sort by

Same author

Structural and Functional Disruption of Thiopurine S‑Methyltransferase by the A80P Variant: A Simulation and Genotyping Study.

ACS omega·2026

Same author

Antagonist Binding Actively Disrupts Interleukin-1 Receptor Dynamics to Block Co-receptor Recruitment.

Computational and structural biotechnology journal·2026

Same author

Blind prediction of complex water and ion ensembles around RNA in CASP16.

bioRxiv : the preprint server for biology·2025

Same author

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.

Proteins·2025

Same author

Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock.

Journal of chemical theory and computation·2025

Same author

Targeted protein degradation in Escherichia coli using CLIPPERs.

EMBO reports·2025

Search research articles

Related Experiment Video

Updated: Jul 4, 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

Structure prediction of linear and cyclic peptides using CABS-flex.

Aleksandra Badaczewska-Dawid¹, Karol Wróblewski², Mateusz Kurcinski²

¹Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, 50011 IA, USA.

Briefings in Bioinformatics

|February 2, 2024

Summary

We developed a new multiscale protocol for peptide structure prediction, combining coarse-grained simulations and all-atom optimization. This method is competitive, especially for short linear peptides, aiding drug discovery and molecular understanding.

Keywords:

cyclic peptides drug design multiscale modeling peptide structural modeling

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

Constructing Cyclic Peptides Using an On-Tether Sulfonium Center

Constructing Cyclic Peptides Using an On-Tether Sulfonium Center

Published on: September 28, 2022

Related Experiment Videos

Last Updated: Jul 4, 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

Constructing Cyclic Peptides Using an On-Tether Sulfonium Center

Constructing Cyclic Peptides Using an On-Tether Sulfonium Center

Published on: September 28, 2022

Area of Science:

Computational biology
Structural biology
Biophysics

Background:

Peptide structural modeling is crucial for drug discovery and understanding molecular mechanisms.
Accurate prediction of peptide structures, including linear and cyclic forms, remains a challenge.

Purpose of the Study:

To present a novel multiscale protocol for predicting the structure of linear and cyclic peptides.
To evaluate the protocol's performance against state-of-the-art tools.

Main Methods:

The protocol integrates coarse-grained simulations (CABS-flex) with all-atom reconstruction-optimization (Modeller).
Evaluation involved sets of linear peptides and cyclic peptides (backbone and disulfide bond cyclization).
Performance was benchmarked against APPTEST, PEP-FOLD, ESMFold, and AlphaFold (ColabFold).

Main Results:

AlphaFold generally provided the highest resolution structures.
The CABS-flex based protocol demonstrated competitive performance, particularly for short linear peptides.
Protocol efficacy can be enhanced by integrating residue-residue contact prediction or improved scoring.

Conclusions:

The novel multiscale protocol offers a valuable tool for peptide and mini-protein structure prediction.
The protocol is accessible via the CABS-flex package with online documentation.
This approach contributes to advancing structural biology and drug discovery efforts.