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Protein-Drug Binding: Determination Methods

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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Updated: Jun 25, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

DruGUI 2.0: Mapping Protein Druggability with Probe-Based Molecular Dynamics.

Carlos Ventura^1,2, Ji Young Lee¹, Anthony T Bogetti^1,3

¹Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.

Bioinformatics (Oxford, England)

|June 24, 2026

Summary

This summary is machine-generated.

DruGUI 2.0 is a new drug discovery tool that identifies druggable protein sites and potential drug molecules. It accounts for protein flexibility and aids in building pharmacophore models for drug development.

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Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

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Last Updated: Jun 25, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

ProDy is an open-source Python package for analyzing protein sequences, structures, and dynamics.
DruGUI 2.0 builds upon the ProDy API to offer advanced drug discovery functionalities.

Purpose of the Study:

To introduce DruGUI 2.0, a novel computational tool for assessing protein druggability.
To facilitate the identification of allosteric and orthosteric binding sites on proteins.
To enable the prediction of small molecules with high binding affinity to target proteins.

Main Methods:

Simulations in explicit solvent, with optional membrane inclusion.
Utilizing an expanded library of drug-like fragments as probe molecules.
Analyzing probe-protein interactions to characterize druggable sites and estimate binding affinities.

Main Results:

DruGUI 2.0 successfully identifies druggable sites beyond traditional orthosteric regions.
The tool predicts small molecules (probes) with high affinity for identified sites.
Pharmacophore models and relative binding affinities can be estimated based on probe composition and position.

Conclusions:

DruGUI 2.0 enhances drug discovery by enabling flexible protein site assessment.
The tool integrates seamlessly with the ProDy ecosystem, offering advanced visualization.
Case studies demonstrate DruGUI 2.0's applicability to both soluble and membrane proteins.