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

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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
PubMed
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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.