Building a virtual ligand screening pipeline using free software: a survey.

Area of Science:

• Computational Chemistry
• Drug Discovery
• Bioinformatics

Background:

• Virtual screening (VS) is crucial for accelerating drug development by computationally identifying bioactive compounds.
• Despite its benefits, VS is underutilized in academic preclinical research, even with growing free resources.
• Commercial VS tools are expensive, limiting access for academic researchers.

Purpose of the Study:

• To survey recent advancements in free virtual screening software and databases.
• To demonstrate how academic researchers can build comprehensive VS pipelines using accessible resources.
• To provide a downloadable, platform-virtualized software system for reproducible VS.

Main Methods:

• Literature review of free virtual screening tools and data repositories.
• Development of a strategy for integrating free resources into a VS pipeline.
• Creation of a downloadable software system using platform virtualization for tool integration.

Main Results:

• Identification of numerous free software and data repositories as viable alternatives to commercial VS tools.
• A framework for constructing integrated VS pipelines on standard academic computing infrastructure.
• A provided software system enabling reproducible VS across different operating systems.

Conclusions:

• Free virtual screening resources are sufficient for academic preclinical research.
• Accessible VS pipelines can significantly reduce drug discovery costs and timelines.
• The provided software system facilitates the adoption and implementation of VS in academia.