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

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

You might also read

Related Articles

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

Sort by
Same author

Structural dissection of the catalytic domain of the serine threonine kinase StkP of Streptococcus pneumoniae.

Nature communications·2026
Same author

An atlas of microtubule lattice parameters regulated through ligand binding to the microtubule-stabilizing sites.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

A quantitative metabolic signature of host response during SARS-CoV-2 infection and recovery.

iScience·2026
Same author

The oncogenic CCDC6-RET fusion protein is a dual ATP- and ADP-dependent kinase.

Nature communications·2026
Same author

A Tetrapodal Tryptophan Derivative with Multiple Exposed Free Carboxylic Acids Blocks Host Cell Entry of Omicron SARS-Cov-2 and Respiratory Syncytial Virus.

ACS omega·2025
Same author

Age- and sex-specific lipoprotein profiles in general and cardiometabolic population cohorts.

EBioMedicine·2025

Related Experiment Video

Updated: May 20, 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

CRDOCK: an ultrafast multipurpose protein-ligand docking tool.

Álvaro Cortés Cabrera1, Javier Klett, Helena G Dos Santos

  • 1Departamento de Farmacología, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.

Journal of Chemical Information and Modeling
|July 7, 2012
PubMed
Summary

CRDOCK is a fast molecular docking and virtual screening program. It achieves high accuracy in predicting ligand binding poses and is useful for drug discovery, particularly for G protein-coupled receptors.

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

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Related Experiment Videos

Last Updated: May 20, 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

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

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Accurate prediction of molecular interactions is crucial for drug discovery.
  • Existing virtual screening tools often face limitations in speed and accuracy.
  • The development of efficient and reliable docking programs is essential for accelerating lead identification.

Purpose of the Study:

  • To introduce CRDOCK, an ultrafast docking and virtual screening program.
  • To present the modular design and capabilities of CRDOCK for customized drug discovery protocols.
  • To evaluate the performance of CRDOCK on established benchmarks and G protein-coupled receptors.

Main Methods:

  • CRDOCK utilizes a search engine with diverse sampling methods and an initial energy evaluation.
  • Energy minimization algorithms and various scoring functions are employed for pose refinement.
  • Ligand conformations are generated from SMILES strings using a precomputed library.

Main Results:

  • CRDOCK achieved a ~75% success rate in pose prediction on the ASTEX diverse set and Directory of Useful Decoys benchmarks.
  • The program demonstrated an average Area Under the Curve (AUC) of 0.66.
  • Ligand docking was performed rapidly, with an average time of ~13 seconds per ligand.

Conclusions:

  • CRDOCK is an effective and efficient tool for molecular docking and virtual screening.
  • The program's modularity allows for optimization of protocols for specific drug discovery challenges.
  • CRDOCK shows utility in screening ligands for G protein-coupled receptors and is integrated into the VSDMIP platform.