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

Conserved Binding Sites01:49

Conserved Binding Sites

4.5K
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...
4.5K
Protein-protein Interfaces02:04

Protein-protein Interfaces

13.9K
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...
13.9K

You might also read

Related Articles

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

Sort by
Same author

Strategic Template Filtering Accelerates Fragment-Based Peptide Docking.

Journal of chemical information and modeling·2026
Same author

Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.

Nature communications·2026
Same author

Identification of ZFTA as a Novel KLHL20 Substrate and Mechanistic Insights Into Fuzzy Binding of Disordered Peptides via Biosensor Analysis and Computational Modelling.

Chembiochem : a European journal of chemical biology·2026
Same author

actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions.

Bioinformatics (Oxford, England)·2025
Same author

Substrate recognition principles for the PP2A-B55 protein phosphatase.

Science advances·2024
Same author

MinD-RNase E interplay controls localization of polar mRNAs in E. coli.

The EMBO journal·2024

Related Experiment Video

Updated: Sep 25, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

395

Matching protein surface structural patches for high-resolution blind peptide docking.

Alisa Khramushin1, Ziv Ben-Aharon1, Tomer Tsaban1

  • 1Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel.

Proceedings of the National Academy of Sciences of the United States of America
|April 28, 2022
PubMed
Summary

PatchMAN models peptide-protein complexes by aligning structural motifs to receptor surfaces, accurately predicting bound peptide conformations without sequence data. This approach significantly outperforms existing methods for peptide docking.

Keywords:
peptide dockingprotein structurestructural motifsstructure matchingsurface complementation

More Related Videos

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

2.0K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.9K

Related Experiment Videos

Last Updated: Sep 25, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

395
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

2.0K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.9K

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biochemistry

Background:

  • Peptide docking is challenging due to peptide flexibility and the need to model both orientation and conformation.
  • Traditional methods often rely on peptide sequence information to generate conformations before docking.

Purpose of the Study:

  • To present PatchMAN (Patch-Motif AligNments), a novel global peptide-docking approach.
  • To accurately model peptide-protein complexes by considering the receptor's structural context.

Main Methods:

  • PatchMAN uses structural motifs and backbone scaffolds from protein structures to map receptor surfaces.
  • It models bound peptide conformation based solely on the receptor's structural context, disregarding peptide sequence information.
  • The method was evaluated on a nonredundant set of protein-peptide complexes starting from free receptor structures.

Main Results:

  • PatchMAN successfully modeled near-native peptide-protein complexes within 2.5 Å/5 Å interface backbone RMSD in 58%/84% of cases.
  • Conformational sampling was achieved in 81%/100% of cases.
  • The approach outperformed existing peptide docking methods.

Conclusions:

  • PatchMAN offers a robust method for peptide docking, accurately predicting bound conformations from receptor structure alone.
  • The approach has implications for studying peptide-protein association principles and designing novel peptide binders.
  • PatchMAN is accessible as a server for broader research use.