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,...

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Ligand Binding Sites

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 Sites

Ligand Binding Sites

Ligand Binding and Linkage

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

You might also read

Related Articles

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

Sort by

Same author

Test-Time Training Scaling Laws for Chemical Exploration in Drug Design.

Journal of chemical information and modeling·2025

Same author

REINFORCE-ING Chemical Language Models for Drug Discovery.

Journal of chemical information and modeling·2025

Same author

Navigating protein landscapes with a machine-learned transferable coarse-grained model.

Nature chemistry·2025

Same author

The Quasi-Bound State as a Predictor of Relative Binding Free Energy.

Journal of chemical information and modeling·2025

Same author

QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials.

Journal of chemical information and modeling·2025

Same author

Broadening the Scope of Neural Network Potentials through Direct Inclusion of Additional Molecular Attributes.

Journal of chemical theory and computation·2025

Search research articles

Related Experiment Video

Updated: Dec 21, 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

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule.

Alejandro Varela-Rial^1,2, Maciej Majewski², Alberto Cuzzolin¹

¹Acellera Labs, Doctor Trueta 183, Barcelona, Spain.

Journal of Chemical Information and Modeling

|May 15, 2020

Summary

This summary is machine-generated.

SkeleDock is a novel scaffold docking algorithm. It accurately predicts protein-ligand binding modes, even outperforming existing software when ligand fragments are available.

More Related Videos

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

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

Related Experiment Videos

Last Updated: Dec 21, 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

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

Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Protein-ligand interactions are crucial for drug discovery.
Accurate prediction of binding modes is essential for identifying novel therapeutics.
Existing docking algorithms face challenges with complex systems like macrocycles and scaffold hopping.

Purpose of the Study:

To introduce and evaluate SkeleDock, a new scaffold docking algorithm.
To assess SkeleDock's performance in predicting protein-ligand binding poses.
To demonstrate SkeleDock's capabilities in modeling macrocycles and scaffold hopping.

Main Methods:

SkeleDock utilizes the structure of a known protein-ligand complex as a template.
The algorithm models the binding mode of chemically similar systems.
Performance was evaluated in the D3R Grand Challenge 4 pose prediction challenge.

Main Results:

SkeleDock achieved competitive performance in the D3R Grand Challenge 4.
SkeleDock outperformed rDock when crystallized ligand fragments were available.
The algorithm demonstrated capacity for modeling macrocycles and scaffold hopping.

Conclusions:

SkeleDock is an effective scaffold docking algorithm for predicting binding modes.
Its performance is enhanced by the availability of crystallized ligand fragments.
SkeleDock offers a valuable tool for drug discovery, particularly for complex molecular systems.