Hybrid MM CG

Hybrid MM CG performs hybrid molecular mechanics/coarse-grained simulations to prepare and model human G protein-coupled receptor (hGPCR)/ligand complexes for analysis of ligand poses and receptor–ligand interactions.

Key Features:

• Automated simulation setup: Integrates atomistic resolution for the ligand, binding cavity, and surrounding water molecules with a coarse-grained representation for the remainder of the receptor to enable dual-resolution simulations.
• Integration with external structural resources: Accepts initial hGPCR/ligand structures generated by other webservers for downstream MM/CG setup.
• Equilibration protocols: Provides fully automatic equilibration procedures for prepared MM/CG systems.
• Analysis outputs: Produces analytical plots summarizing simulation properties and system characteristics.

Scientific Applications:

• hGPCR pharmacology: Enables investigation of receptor–ligand interactions in human G protein-coupled receptors relevant to pharmacological research.
• Ligand pose prediction: Supports prediction and refinement of ligand poses within GPCR binding cavities using atomistic treatment of the binding site.
• Molecular dynamics of GPCR/ligand complexes: Facilitates atomistic and coarse-grained molecular dynamics exploration of receptor–ligand interactions.
• Drug discovery and development: Supports structure-based investigation relevant to drug discovery and development workflows targeting GPCRs.

Methodology:

The methodology uses a hybrid Molecular Mechanics (MM)/Coarse-Grained (CG) approach with atomistic treatment of the ligand, binding cavity, and surrounding water molecules and a coarse-grained representation for the remainder of the receptor, together with equilibration protocols for the prepared systems.