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

5.0K
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...
5.0K

You might also read

Related Articles

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

Sort by
Same author

Atomic basis for functional evolution of plant lanosterol synthase.

The New phytologist·2025
Same author

[Advances in the catalytic promiscuity of nitrilases].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology·2025
Same author

AromTool: predicting aromatic stacking energy using an atomic neural network model.

Physical chemistry chemical physics : PCCP·2021
Same author

Multiscale Simulations on the Catalytic Plasticity of CYP76AH1.

Frontiers in chemistry·2021
Same author

TeroKit: A Database-Driven Web Server for Terpenome Research.

Journal of chemical information and modeling·2020
Same author

Deciphering the mechanisms of selective inhibition for the tandem BD1/BD2 in the BET-bromodomain family.

Physical chemistry chemical physics : PCCP·2017

Related Experiment Video

Updated: Dec 22, 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

808

GM-DockZn: a geometry matching-based docking algorithm for zinc proteins.

Kai Wang1,2, Nan Lyu1, Hongjuan Diao1

  • 1Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006.

Bioinformatics (Oxford, England)
|May 6, 2020
PubMed
Summary
This summary is machine-generated.

We developed GM-DockZn, a new tool for docking ligands to zinc proteins. It outperforms existing methods in accurately predicting ligand-protein interactions, especially for metalloproteins.

More Related Videos

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

979
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.7K

Related Experiment Videos

Last Updated: Dec 22, 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

808
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

979
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.7K

Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Molecular docking is crucial for virtual screening but struggles with metalloproteins.
  • Zinc proteins represent a significant portion of protein structures, highlighting the need for specialized tools.

Purpose of the Study:

  • To develop GM-DockZn, a novel computational tool specifically designed for ligand docking to zinc proteins.
  • To address the limitations of existing docking methods in handling the complexities of metalloprotein interactions.

Main Methods:

  • GM-DockZn employs a geometry-based approach, sampling ligand conformations around ideal zinc-coordination positions.
  • Identified seven conserved coordination motifs from known zinc-ligand complexes to guide sampling.

Main Results:

  • GM-DockZn demonstrated superior performance in sampling near-native poses compared to state-of-the-art techniques.
  • Achieved high accuracy in predicting correct coordination atoms and numbers within top predictions for diverse zinc protein systems.
  • Combining GM-DockZn with GOLD for ranking yielded the highest success rates for near-native pose prediction.

Conclusions:

  • GM-DockZn offers a significant advancement for docking studies involving zinc proteins.
  • The geometry-based sampling strategy shows promise for application to other metalloproteins.
  • GM-DockZn is freely available for academic use, facilitating further research in metalloprotein-ligand interactions.