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Updated: Jun 14, 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

VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters.

Nikita D Prakhov¹, Alexander L Chernorudskiy, Murat R Gainullin

¹Faculty of Biology, Nizhny Novgorod State University, 23 Gagarin Avenue, 603950 Nizhny Novgorod, Russia. nikita.prakhov@gmail.com

Bioinformatics (Oxford, England)

|April 10, 2010

Summary

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VSDocker is a new program for optimized virtual ligand screening using AutoDock4 on computer clusters. It is the first tool for high-performance virtual screening on Windows systems.

Area of Science:

Computational chemistry
Drug discovery
Bioinformatics

Background:

VSDocker 2.0 is available for non-commercial use.
Contact information and supplementary data are provided.

Purpose of the Study:

To introduce VSDocker, a novel program for virtual ligand screening.
To enable optimized virtual screening on computer clusters and multiprocessor workstations.

Main Methods:

Utilizes AutoDock4 for virtual screening.
Implements parallel processing for high-performance computing.

Main Results:

VSDocker facilitates optimized virtual ligand screening.
It is the first implementation for MS Windows-based systems.

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Conclusions:

VSDocker is an original and efficient tool for virtual ligand screening.
It enhances computational drug discovery capabilities on Windows platforms.