PLIDflow: an open-source workflow for the online analysis of protein-ligand docking using galaxy

Area of Science:

• Computational chemistry
• Structural biology
• Drug discovery

Background:

• Molecular docking predicts small-molecule (ligand) binding to target proteins.
• Accurate binding site (BS) identification is crucial but often unknown.
• Current methods require multiple programs, complex parameters, and significant computational resources.

Purpose of the Study:

• To develop an automated computational workflow (WF) for protein-ligand complex analysis.
• To streamline the process from binding site identification to binding mode and affinity prediction.
• To provide an accessible tool for researchers without extensive computational backgrounds.

Main Methods:

• Designed an automatic computational workflow (WF) integrated into the Galaxy platform.
• Integrated public domain software for seamless execution.
• Workflow covers binding site identification and protein-ligand docking.

Main Results:

• The proposed WF automates protein-ligand complex processing.
• Achieved close agreement with state-of-the-art docking software.
• Provides accurate prediction of binding modes and affinities.

Conclusions:

• The automated workflow simplifies complex molecular docking simulations.
• Enhances accessibility for researchers in drug discovery and biochemistry.
• Offers a valuable tool for protein engineering and computational drug design.