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

Assembly of Signaling Complexes

Assembly of Signaling Complexes

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,...

You might also read

Related Articles

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

Sort by

Same author

Deep learning-enabled discovery of antibiotics effective against <i>Neisseria gonorrhoeae</i>.

Science translational medicine·2026

Same author

Structural basis for uracil removal from DNA by human SMUG1.

Nature communications·2026

Same author

Toward a Random Background for Ligand Optimization.

bioRxiv : the preprint server for biology·2026

Same author

Local GPCR density tips the balance of μ-opioid receptor trafficking.

bioRxiv : the preprint server for biology·2026

Same author

The Selectivity Implications of Docking Libraries with Greater and Lesser Similarities to Bio-like Molecules.

Journal of medicinal chemistry·2026

Same author

Improving AlphaFold2 Performance in Virtual Screens Targeting GPCRs by Enhancing Binding-Site Conformational Sampling.

Journal of chemical information and modeling·2026

Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026

Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026

Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026

Same journal

Multimodal imaging and quantification of lanthanide chelate-labeled micro- and nanoplastics in plants.

Nature protocols·2026

Same journal

Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform.

Nature protocols·2026

Same journal

Yeast nuclei-mediated precise delivery of synthetic megabase-scale human DNA into mammalian embryos.

Nature protocols·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 19, 2025

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

A practical guide to large-scale docking.

Brian J Bender¹, Stefan Gahbauer¹, Andreas Luttens²

¹Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.

Nature Protocols

|September 25, 2021

Summary

This summary is machine-generated.

Structure-based virtual screening using molecular docking allows rapid exploration of vast chemical libraries for drug discovery. Implementing control docking calculations enhances success rates and identifies potent compounds, as demonstrated with the melatonin receptor.

More Related Videos

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

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

Published on: June 20, 2025

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

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

Published on: February 23, 2024

Related Experiment Videos

Last Updated: Oct 19, 2025

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

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

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

Published on: June 20, 2025

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

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

Published on: February 23, 2024

Area of Science:

Computational chemistry
Drug discovery
Molecular modeling

Background:

Structure-based virtual screening is crucial for early drug and probe discovery.
Advancements in computing power enable screening of billions of compounds.
Approximations in docking can lead to undersampling and inaccurate binding energy predictions.

Purpose of the Study:

To outline best practices and control docking calculations for evaluating docking parameters.
To enhance the success likelihood of large-scale prospective screens.
To provide guidelines for ensuring specific activity of validated hit compounds.

Main Methods:

Development and application of control docking calculations.
Evaluation of docking parameters for specific targets prior to large-scale screening.
Exemplification using the DOCK3.7 software on the melatonin receptor target.

Main Results:

The outlined procedure led to direct docking hits with subnanomolar activity for the melatonin receptor.
Control calculations helped evaluate docking parameters effectively.
Guidelines were established to ensure specific activity for validated hits.

Conclusions:

Implementing control docking calculations is essential for successful large-scale virtual screening.
Best practices improve the reliability of hit identification in drug discovery.
The DOCK3.7 software is available for academic research to explore new drug targets.