Collaborative Science

Accelerating time to market and driving innovation with collaboration, knowledge based under-standing and prediction.

Simulations

BIOVIA Discovery Studio includes the highly versatile CHARMm molecular mechanics simulation program. With over 30 years of peer-review academic research, CHARMm has been developed with a primary focus on the study proteins, peptides, small molecule ligands, nucleic acids, lipids and carbohydrates.

For Quantum Mechanics-based studies, BIOVIA Discovery Studio includes the DMol3 program. DMol3 is a DFT program with a long track record of successful commercial applications. With its unique approach to solving quantum mechanical equations, DMol3 has long been one of the fastest methods available for performing calculations, an advantage that becomes apparent especially for larger systems, those with over 500 atoms.

Discovery Studio includes tools for:

  • Molecular Mechanics (MM) calculations using CHARMm c40b1
  • Support for a broad range of force fields, including CGenFF, charmm36, charmm27, charmm22, CHARMm, CHARMm-polarH, CFF, MMFF and more
  • Perform quick and accurate protein ionization and residue pKs using a CHARMm Generalized-Born (GB) solvent model
  • Fast explicit aqueous solvation method with optional counter-ions suitable for very large molecular systems
  • Perform either explicit solvent or implicit GB solvent-based Molecular Mechanics (MM) minimizations
  • Perform either explicit solvent or implicit solvent-based Molecular Dynamics (MD) simulations
  • Add an implicit membrane to a protein structure to help refine models during forcefield-based simulations
  • Alternatively, launch a NAMD calculation and perform MD simulations
  • Perform pose optimization of multiple ligands in the context of a receptor with a static or flexible receptor
  • Use CDOCKER, a CHARMm-based docking engine to perform flexible ligand-based docking and docking refinement
  • Score binding interactions with MM-PBSA or MM-GBSA CHARMm-based methods
  • Calculate single point energies or perform minimizations of receptor-ligand complexes using hybrid Quantum Mechanics (QM)/MM simulations
  • Estimate ligand binding free energy and study ligand unbinding using CHARMm-based Steered Molecular Dynamics (SMD) simulations

Read the Discovery Studio Simulations Datasheet