PoseFilter: a PyMOL plugin for filtering and analyzing small molecule docking in symmetric binding sites.

Area of Science:

• Computational Biology
• Structural Bioinformatics
• Drug Discovery

Background:

• Protein-ligand docking is crucial for drug discovery.
• Analyzing large numbers of docked poses can be challenging.
• Identifying symmetric poses is important for oligomeric complexes.

Purpose of the Study:

• To introduce PoseFilter, a novel PyMOL plugin.
• To facilitate the analysis and filtering of docked poses.
• To enable automatic detection of symmetric poses.

Main Methods:

• PoseFilter is a PyMOL plugin with a graphical user interface and command-line options.
• It implements methods for root mean square deviation (RMSD) analysis.
• It incorporates interaction fingerprint analysis for pose comparison.

Main Results:

• PoseFilter successfully automates the detection of symmetric poses.
• The plugin provides robust tools for analyzing docking outputs.
• Its capabilities are demonstrated on various oligomeric protein-ligand complexes.

Conclusions:

• PoseFilter streamlines the analysis of protein-ligand docking poses.
• The plugin enhances the efficiency of virtual screening workflows.
• It is a valuable tool for researchers in computational chemistry and drug design.