Single-click molecular docking via SwiftDock: A new virtual screening tool using AutoDock4
Billel Larbaoui, Rafik Menad · Computational and Structural Biotechnology Reports · 2024
Molecular Docking (MD) is employed to predict protein-ligand interactions. It can be executed using a variety of software tools, including AutoDock4 (AD4), AutoDock Vina (ADV), FlexX, GOLD, and MVD. MD is particularly useful for its application in virtual screening (VS), which involves docking small molecules to a macromolecule to identify lead compounds with the desired biological activity. VS can be performed using software such as PyRx, InstaDock, and MultiDock Screening Tool, predominantly utilizing ADV. Among these tools, InstaDock is particularly distinguished for its single-click execution. While there are software and scripts available that can automate various stages of VS via AD4, there is currently no tool available that can execute an entire AutoDock4-based VS with a single click, handling the entire workflow from protein and ligand preparation to optimal pose extraction. In this article, we introduce SwiftDock ( https://github.com/notacoder-dz/SwiftDock ), a new open-source VS tool for Windows users capable of performing VS with AD4 in a single-click manner, minimizing user intervention and requiring no prior software knowledge (MGLTools, OpenBabel, and AD4). For demonstration purposes, the software was placed in a target folder containing protein and ligand files. Upon execution, a series of operations were automatically performed, ranging from file preparation to post-docking extraction of the lowest binding energies and corresponding poses, utilizing pre-installed software. Despite its limitations, SwiftDock represents a promising tool that can enhance accessibility to MD and VS for non-bioinformaticians, thereby facilitating experimental and therapeutic research, with potential for future enhancements.