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Automated Workflows

  • drMD: drMD: Molecular Dynamics for Experimentalists
    Code Last Commit Publication
  • Enlighten2: Protocols and tools to run (automated) atomistic simulations (molecular dynamics) of enzyme-ligand systems (Python, PyMOL plugin, standalone)
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  • StreaMD: streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis
    Code Last Commit Publication

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
    Code Last Commit Publication