Automated Workflows

• Enlighten2: Protocols and tools to run (automated) atomistic simulations (molecular dynamics) of enzyme-ligand systems (Python, PyMOL plugin, standalone)

• StreaMD: streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis
  

  

• drMD: drMD: Molecular Dynamics for Experimentalists
  

  

Ligand Stability

• MDFit: protein–ligand compatibility, including stability of different ligand-pocket interactions and other useful metrics that enable easy rank-ordering of the ligand library for pocket optimization