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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 analyses the...

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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Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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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Ligand Binding Sites

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Related Experiment Video

Updated: May 23, 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

Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking

Michael T Zimmermann¹, Sumudu P Leelananda, Andrzej Kloczkowski

¹Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, Iowa 50011, USA.

The Journal of Physical Chemistry. B

|April 12, 2012

Summary

Evaluating protein structures and docking poses is crucial. This study introduces a new method using statistical potentials and dynamics to improve the accuracy of selecting native-like protein structures and docking poses.

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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

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Last Updated: May 23, 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 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 structure prediction and protein-protein docking are vital tools in molecular biology.
Current methods for evaluating predicted protein structures and docking poses have limitations, often relying on energy functions that can fail.
Improved structure evaluation is essential for advancing these fields.

Purpose of the Study:

To develop and validate an enhanced method for evaluating the quality of predicted protein structures and protein-protein docking poses.
To improve the accuracy of identifying native-like structures and the best docking poses.

Main Methods:

Combined multibody statistical potentials with dynamics models.
Evaluated fluctuation-based entropies, incorporating contributions from the entire protein structure.
Applied the method to CASP9 protein structure prediction decoys and various protein-protein docking datasets (ClusPro, Benchmark 3.0, Dockground).

Main Results:

Demonstrated enhanced selection of native-like structures for CASP9 decoys.
Achieved refined protein-protein docking poses across multiple benchmark datasets.
Showed positive results for both bound and unbound docking scenarios.
Frequently identified the top-ranked pose for high-quality docking predictions.

Conclusions:

The novel approach integrating statistical potentials and dynamics models significantly improves the evaluation of protein structures and docking poses.
This method offers a more reliable way to assess structural predictions and binding interactions.
The findings pave the way for more accurate computational modeling in structural biology.