StreaMD

StreaMD streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis of protein, ligand, and protein-ligand complex systems including co-factors.

Key Features:

• Automated simulation workflow: Automates preparation, execution, and analysis of molecular dynamics trajectories with minimal user intervention.
• Distributed computing: Efficiently operates across multiple servers within a network or a cluster for large-scale simulations.
• Binding free energy calculation: Seamlessly integrates with MM-GBSA/PBSA methods for computing free binding energies of protein-ligand complexes.
• Interaction fingerprinting: Generates protein-ligand interaction fingerprints across the trajectory.
• Multi-system compatibility: Applicable to proteins, ligands, and their complexes including co-factors.

Scientific Applications:

• Protein dynamics studies: Investigates the dynamic behaviour of proteins through classical molecular dynamics simulations.
• Protein-ligand interaction analysis: Analyzes dynamic behaviour and binding characteristics of protein-ligand complexes.
• High-throughput compound screening: Enables large-scale molecular dynamics simulations for extensive compound sets.
• Binding affinity prediction: Computes free binding energies to assess protein-ligand binding affinities using MM-GBSA/PBSA approaches.

Methodology:

StreaMD is a Python-based tool that uses GROMACS as the underlying simulation engine and automates trajectory simulation, MM-GBSA/PBSA binding free energy calculation, and protein-ligand interaction fingerprint generation.