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Conserved Binding Sites

Conserved Binding Sites

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.
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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...

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Related Experiment Video

Updated: Jan 16, 2026

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

Protein-Ligand Structure Prediction by Template-Guided Ensemble Docking Strategy.

Keqiong Zhang¹, Qilong Wu¹, Sheng-You Huang¹

¹School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.

|October 6, 2025

Summary

This summary is machine-generated.

This study introduces a template-guided ensemble docking strategy for protein-ligand structure prediction in CASP16. The novel approach achieved a 4th place ranking among 38 teams, demonstrating its effectiveness in predicting ligand binding poses.

Keywords:

CASP drug discovery ligand binding molecular docking protein–ligand complex template‐based docking

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Last Updated: Jan 16, 2026

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

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Published on: July 25, 2013

Area of Science:

Computational biology
Structural biology
Drug discovery

Background:

The Critical Assessment of Techniques for Structure Prediction (CASP) introduced protein-ligand complex structure prediction in CASP15.
CASP16 expanded this category with pharmaceutical super-targets, each comprising a protein with multiple ligands.

Purpose of the Study:

To develop and evaluate a template-guided ensemble docking strategy for the ligand (LG) tasks in CASP16.
To leverage recent advancements in protein structure prediction for improved protein-ligand complex modeling.

Main Methods:

Generated structural ensembles using MODELER, AlphaFold3, and AlphaFold-Multimer.
Searched the Protein Data Bank (PDB) for templates using sequence identity, ligand similarity, and Maximum Common Substructure (MCS).
Employed LSalign for 3D ligand alignment, XDock and MDock for template-free predictions, and ITScore for energy evaluation.

Main Results:

The developed method ranked 4th out of 38 participating teams in the CASP16 LG tasks.
The template-guided ensemble docking strategy proved effective for protein-ligand structure prediction.
Successful integration of multiple structure prediction tools and template-based approaches.

Conclusions:

The template-guided ensemble docking strategy is a robust method for protein-ligand complex structure prediction.
The approach shows significant promise for drug discovery and development pipelines.
Performance in CASP16 validates the strategy's potential in advancing structural biology techniques.