Simulations

INCLUDES THE HIGHLY VERSATILE CHARMm MOLECULAR MECHANICS SIMULATION PROGRAM

Biomolecular processes rely on a variety of dynamic interactions between proteins, ligands, solvents and ions. Often, the specifics of these interactions are difficult to capture via physical experimentation alone due to the short time scales over which they occur. Simulation can help elucidate the energetics of these processes, providing insight into their mechanism of action and properties.

Discovery Studio utilizes the highly versatile CHARMm molecular simulation program. With over 30 years of peer-reviewed academic research, CHARMm targets the study of biological systems such as proteins, peptides, small molecule ligands, nucleic acids, lipids and carbohydrates.

Simulate
  • CHARMm
    • Perform explicit solvent or implicit solvent-based minimizations and Molecular Dynamics (MD) simulations
    • GPU-enabled via DOMDEC and OpenMM
  • NAMD
    • Perform explicit solvent MD simulations
    • Solvate a protein with explicit membrane and run MD simulations
  • DMol3 / CHARMm
    • Calculate single point energies or perform minimizations of receptor-ligand complexes using hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) simulations
Model
  • Support for a broad range of force fields, including CGenFF, charmm36, CHARMm and more
  • MATCH method for typing ligands with charmm36
  • Full support of CHARMM patching mechanism
  • Fast explicit aqueous solvation method with optional counter-ions suitable for very large molecular systems
  • Solvation of transmembrane protein into pre-equilibrated lipid bilayer
  • Analysis of MD trajectories
Explore
  • Perform quick and accurate protein ionization and residue pKs predictions for protein preparation
  • Use CDOCKER, a CHARMm-based docking engine to perform flexible ligand-based docking and refinement
  • Perform pose optimization of multiple ligands in the context of a receptor
  • Calculate binding energies of docked poses
  • Accurately predict relative ligand binding energy for a congeneric ligand series using the free energy perturbation (FEP) method
  • Calculate the relative free energy of binding for a combinatorial library of ligands modeled by Multi-Site Lambda Dynamics (MSLD)
  • Estimate ligand binding free energy and study ligand unbinding using CHARMm-based Steered Molecular Dynamics (SMD) simulations
  • Examine electrostatic potential effects with CHARMm Poisson-Boltzmann (PB) equation