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Related Concept Videos

The Equilibrium Binding Constant and Binding Strength02:18

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:
Ligand Binding Sites02:40

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 Sites02:40

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...
Protein-Drug Binding: Determination Methods01:22

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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Related Experiment Video

Updated: Jul 3, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

BFEE-Docking: A User-Friendly and Customizable End-to-End Tool from High-Throughput Virtual Screening to Binding

Xiwen Sun1,2, Zihong Li3, Xueguang Shao1,2

  • 1Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.

Journal of Chemical Theory and Computation
|July 2, 2026
PubMed
Summary

BFEE-docking is a new open-source platform that automates drug discovery workflows, connecting virtual screening to free energy calculations. It enables easier customization and identifies novel drug candidates, like potential inhibitors for EGFR.

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Last Updated: Jul 3, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Published on: June 20, 2025

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Rational drug design relies on sequential virtual screening, redocking, and free energy calculations.
  • Existing tools are specialized, and integrated platforms often lack accessibility.
  • There is a need for an open-source, user-friendly platform connecting these stages.

Purpose of the Study:

  • To develop BFEE-docking, an integrated, automated drug discovery workflow platform.
  • To extend the capabilities of BFEE3 for seamless virtual screening to free energy evaluation.
  • To provide a customizable and accessible tool for drug discovery specialists and nonspecialists.

Main Methods:

  • Developed BFEE-docking, a cross-platform software companion to BFEE3.
  • Automated GPU-accelerated virtual screening, flexible redocking, and MM-GBSA or ABFE calculations.
  • Integrated PyMOL for real-time visualization and on-the-fly protocol customization.

Main Results:

  • BFEE-docking automates complex preparation tasks like protonation and binding site identification.
  • The platform successfully performed binding free-energy calculations within a screening workflow for EGFR.
  • Identified two novel potential inhibitors missed in previous studies.

Conclusions:

  • BFEE-docking provides a reliable and effective integrated platform for drug discovery.
  • The software enhances accessibility and customization in computational drug design.
  • Demonstrated utility in identifying novel drug candidates through automated workflows.