OpenMMDL

OpenMMDL prepares and simulates protein-ligand complexes in OpenMM and analyzes protein-ligand interactions.

Key Features:

• Protein-ligand complex preparation: Prepares protein and simulation settings for receptor-ligand systems.
• MD simulation: Performs molecular dynamics simulations with consecutive trajectory postprocessing.
• Ligand binding analysis: Analyzes simulation results with respect to ligand binding and generates ligand binding modes throughout simulations.
• Water molecule tracking: Tracks and clusters water molecules, particularly those exhibiting minimal displacement from their previous coordinates, providing insights into solvent dynamics.

Scientific Applications:

• Kinase-ligand interactions: Studied LDN-193189 and LDN-212854 with ALK2.
• Ion channel-ligand interactions: Studied nifedipine and amlodipine in Cav1.1.
• GPCR-ligand interactions: Studied LSD in 5-HT2B.
• Cytochrome P450-ligand interactions: Studied letrozole in CYP19A1.
• RNA-ligand interactions: Studied flavin mononucleotide binding the FMN-riboswitch.
• Toll-like receptor-ligand interactions: Studied ligand C08 bound to TLR8.
• Opioid receptor-ligand interactions: Studied PZM21 bound to MOR.

Methodology:

OpenMMDL consists of three main components: OpenMMDL Setup based on Python Flask to prepare protein and simulation settings, OpenMMDL Simulation to perform MD simulations with consecutive trajectory postprocessing, and OpenMMDL Analysis to analyze simulation results with respect to ligand binding.