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

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

You might also read

Related Articles

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

Sort by

Same author

PIP<sub>2</sub> activation of the cardiac I<sub>Ks</sub> potassium channel.

Nature communications·2026

Same author

Docking-based virtual screening: Past, present, and future.

Biophysical journal·2026

Same author

Polymerization-mediated SRFR1 condensation in upper lateral root cap cells regulates root growth.

The Plant cell·2025

Same author

A lightweight tunnel vehicle re-ldentification model based on YOLOv11n and FaceNet.

PloS one·2025

Same author

PIP<sub>2</sub> activation of the cardiac I<sub>Ks</sub> potassium channel.

Research square·2025

Same author

Performance of Hybrid Strategies Combining MDockPP and AlphaFold2 in CAPRI Rounds 47-55.

Proteins·2025

Search research articles

Related Experiment Video

Updated: Jan 2, 2026

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

PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.

Xianjin Xu^1,2,3,4, Xiaoqin Zou^1,2,3,4

¹Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.

Journal of Computational Chemistry

|December 4, 2019

Summary

A new benchmark, PepPro, offers 89 nonredundant peptide-protein complex structures for testing docking algorithms. This resource aids in developing better computational methods for peptide-protein interactions.

Keywords:

benchmark peptide docking protein-peptide complexes protein-peptide docking protein-peptide interactions

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

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

Related Experiment Videos

Last Updated: Jan 2, 2026

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

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

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

Area of Science:

Structural Biology
Computational Chemistry
Bioinformatics

Background:

Peptide-protein interactions are crucial in biological processes.
Accurate prediction of these interactions requires robust computational tools.
Existing benchmarks may lack diversity or nonredundancy for comprehensive algorithm testing.

Purpose of the Study:

To introduce PepPro, a novel, nonredundant benchmark dataset for evaluating peptide-protein docking algorithms.
To provide a diverse set of experimentally determined peptide-protein complex structures.
To facilitate the development and improvement of computational docking methods.

Main Methods:

Compilation of 89 nonredundant experimentally determined peptide-protein complex structures.
Inclusion of peptides with varying lengths (5-30 amino acids) and diverse secondary structures (helix, beta-sheet, coil).
Provision of unbound protein structures for 58 complexes to assess handling of conformational changes.

Main Results:

The PepPro benchmark comprises 89 unique peptide-protein complexes.
It covers a wide range of peptide secondary structures and binding modes.
Includes unbound protein structures for 58 cases, enabling assessment of protein flexibility in docking.

Conclusions:

PepPro serves as a valuable resource for the peptide-protein docking community.
The benchmark's diversity and nonredundancy will drive advancements in docking algorithm performance.
It supports the development of more accurate computational models for predicting peptide-protein recognition.