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Updated: Jul 7, 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

DOCKweb: a web-based GUI platform for molecular modeling with DOCK6.

Steven Pak¹, Brock T Boysan², William J Allen³

¹Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA.

Journal of Computer-Aided Molecular Design

|July 6, 2026

Summary

This summary is machine-generated.

We developed DOCKweb, a web application simplifying virtual screening (VS) and de novo design (DN) using DOCK6. This tool makes complex computational drug discovery accessible to all users, regardless of technical expertise.

Keywords:

Computer-aided drug design DOCK6 De novo design Graphical-user interface Molecular modeling Virtual screening Web application

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

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New Features in Visual Dynamics 3.0

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Area of Science:

Computational chemistry
Cheminformatics
Drug discovery

Background:

Virtual screening (VS) and de novo design (DN) are essential computational methods for identifying drug leads.
Existing tools like DOCK6 require command-line expertise, limiting accessibility for many researchers.
Streamlining these processes can accelerate the drug discovery pipeline.

Purpose of the Study:

To develop a user-friendly web application, DOCKweb, for the DOCK6 software.
To simplify the setup and submission of DOCK6 calculations.
To broaden access to advanced computational drug discovery tools.

Main Methods:

Developed a full-stack web application (DOCKweb) using React.js and Express.js.
Created an interactive graphical user interface (GUI) to streamline DOCK6 usage.
Integrated DOCK6 calculations with the Texas Advanced Computer Center (TACC) for remote execution.

Main Results:

DOCKweb provides an intuitive GUI, eliminating the need for command-line proficiency.
Users can submit DOCK6 calculations without local software installation or compilation.
Remote computation via TACC removes the necessity for users to possess supercomputing resources.

Conclusions:

DOCKweb significantly lowers the barrier to entry for utilizing DOCK6 for VS and DN.
The application democratizes access to powerful computational drug discovery tools.
DOCKweb facilitates broader adoption and application of DOCK6 in drug lead identification.