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

Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

6.7K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
6.7K

You might also read

Related Articles

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

Sort by
Same author

Measurement of feline-specific pancreatic lipase aids in the diagnosis of pancreatitis in cats.

Journal of the American Veterinary Medical Association·2023
Same author

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.

Proteomics·2023
Same author

EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning.

Journal of molecular biology·2023
Same author

Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions.

PLoS computational biology·2023
Same author

Reduced B cell antigenicity of Omicron lowers host serologic response.

Cell reports·2022
Same author

ScanNet: A Web Server for Structure-based Prediction of Protein Binding Sites with Geometric Deep Learning.

Journal of molecular biology·2022
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Feb 23, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.3K

SnapDock-template-based docking by Geometric Hashing.

Michael Estrin1, Haim J Wolfson1

  • 1Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

Bioinformatics (Oxford, England)
|September 9, 2017
PubMed
Summary
This summary is machine-generated.

SnapDock, a template-based protein-protein docking algorithm, achieves 35% success in re-modeling PDB complexes. Combining it with PatchDock boosts success to 42%, offering an efficient approach for protein interaction studies.

More Related Videos

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

1.2K
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.8K

Related Experiment Videos

Last Updated: Feb 23, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.3K
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

1.2K
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.8K

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biochemistry

Background:

  • Protein-protein interactions are crucial in biological processes.
  • Accurate prediction of protein complex structures is essential for understanding function.
  • Existing protein docking methods face challenges in efficiency and accuracy.

Purpose of the Study:

  • To introduce SnapDock, a novel, highly efficient template-based protein-protein docking algorithm.
  • To evaluate SnapDock's performance against existing methods, including a flexible docking approach.
  • To explore the synergistic potential of combining SnapDock with template-free docking algorithms.

Main Methods:

  • Utilizes Geometric Hashing for structural alignment to protein-protein interface libraries (PIFACE).
  • Performs docking using a library of 22,600 interfaces, achieving average docking times under 2 minutes.
  • Incorporates a flexible docking version allowing hinge motion in one protein.

Main Results:

  • Achieved a 35% success ratio in blind re-modeling of 3547 Protein Data Bank (PDB) complexes.
  • SnapDock outperformed the template-free PatchDock algorithm (23% success rate).
  • Combining SnapDock with PatchDock yielded a 42% success ratio, demonstrating synergistic effects.

Conclusions:

  • SnapDock offers a significant advancement in efficient and accurate protein-protein docking.
  • The combination of template-based and template-free methods presents a promising strategy for improving docking accuracy.
  • Further development includes a web server for broader accessibility.