CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs

Area of Science:

• Computational chemistry
• Structural biology
• Drug discovery

Background:

• Molecular docking is crucial for identifying ligand-receptor binding poses in drug discovery.
• Preparing docking systems is a complex, time-consuming bottleneck.
• Reproducibility in docking studies is often challenging.

Purpose of the Study:

• To develop an automated, user-friendly platform for molecular docking and simulation system preparation.
• To integrate multiple popular docking engines into a single framework.
• To streamline the process of generating simulation-ready systems from docking results.

Main Methods:

• Development of CHARMM-GUI Ligand Docker, a web-based tool.
• Integration of AutoDock Vina, Smina, RxDock, and DiffDock.
• Inclusion of PoseBuster for filtering docking poses.
• Seamless transfer of poses to CHARMM-GUI High-Throughput Simulator.

Main Results:

• CHARMM-GUI Ligand Docker provides a unified interface for docking calculations.
• The platform simplifies receptor and ligand structure preparation and binding site definition.
• Automated filtering and transfer to simulation workflows enhance reproducibility and efficiency.

Conclusions:

• Ligand Docker significantly simplifies and accelerates the setup of molecular docking and simulation workflows.
• The tool bridges the gap between docking and molecular dynamics simulations.
• It serves as a valuable web resource for both expert and non-expert users in drug discovery.