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Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and

Faizul Azam1, Suliman A Almahmoud1

  • 1Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia.

International Journal of Molecular Sciences
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PubMed
Summary

Open-source molecular docking tools are advancing computational drug discovery. These resources, enhanced by AI, streamline workflows from study design to virtual screening for reproducible research.

Keywords:
artificial intelligencemolecular dockingopen-source softwarereproducible workflowsstructure-based drug designvirtual screening

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Molecular docking is crucial for drug discovery, aiding in binding hypotheses, compound prioritization, and target selectivity.
  • Advancements in open-source tools, scoring functions, and hardware have increased accessibility for research and education.

Purpose of the Study:

  • To review open-source molecular docking resources and workflows.
  • To evaluate the integration of AI methods into docking pipelines.
  • To provide a framework for effective use of docking and virtual screening in drug discovery.

Main Methods:

  • Workflow-centered analysis of open-source docking resources.
  • Examination of AI-augmented methods for pose prediction, rescoring, and virtual screening.
  • Evaluation of tools for study design, data acquisition, and validation.

Main Results:

  • The open-source ecosystem now includes browser-accessible tools, preparation utilities, and AI-enhanced methods.
  • Docking workflows are becoming more accessible, customizable, and transparent.
  • AI integration expands structural coverage and improves screening efficiency.

Conclusions:

  • Open-source molecular docking and AI offer a practical framework for modern drug discovery.
  • These advancements facilitate reproducible research and early-stage hit identification.
  • Effective utilization of these pipelines supports contemporary structure-based drug design.