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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.
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...

Conserved Binding Sites

Conserved Binding Sites

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Related Experiment Video

Updated: Feb 28, 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

Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches.

Stefano Motta¹, Laura Bonati¹

¹Department of Earth and Environmental Sciences, University of Milano-Bicocca , Piazza della Scienza 1, 20126 Milan, Italy.

Journal of Chemical Information and Modeling

|June 16, 2017

Summary

This study shows ensemble-docking accurately predicts ligand-protein complex structures by carefully selecting methods based on protein motion and binding mechanisms, like conformational selection and induced fit.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational Biology
Structural Biology
Biophysics

Background:

Protein dynamics are crucial for ligand binding and molecular recognition.
Understanding protein motion is key to accurate prediction of binding geometry.
Ensemble-docking approaches require careful methodological choices.

Purpose of the Study:

To elucidate critical choices in ensemble-docking for predicting ligand-protein binding geometry.
To investigate ligand-binding processes involving large protein conformational changes.
To compare conformational selection and induced-fit mechanisms in two distinct binding systems.

Main Methods:

Ensemble-docking technique applied to apo protein simulations.
Accelerated molecular dynamics (MD) simulations for conformational sampling.
Geometric clustering strategy for binding site conformation selection.
Case studies: acetylcholine binding protein and allose binding protein.

Main Results:

Ensemble-docking reliably predicts ligand-protein complex structures with appropriate methodological choices.
Accelerated MD simulations effectively sample conformations across high energy barriers when parameters are optimized.
Geometric clustering efficiently identifies relevant binding site conformations from MD trajectories.
Ligand-induced protein flexibility requires specific strategies in docking and pose refinement.

Conclusions:

Ensemble-docking is a reliable method for predicting ligand-protein complex structures.
Methodological choices in ensemble-docking must align with specific protein dynamics and binding mechanisms.
Accelerated MD and geometric clustering are valuable tools for conformational sampling and selection in binding studies.