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Welcome to the PyRod wiki!

This wiki is intended to give short information about PyRod installation and usage.

PyRod is a free open-source python software that generates dynamic molecular interaction fields (dMIFs) based on tracing water molecules in MD simulations. For each frame the environment of each water molecule is analyzed for potential interaction partners to form e.g. hydrogen bonds. As water molecules may also fill hydrophobic pockets or interact with charged residues, the environment is also analyzed for hydrophobic, aromatic and charged residues. This information is saved and averaged in a grid throughout the trajectory. The dMIFs are saved as density maps and can be visualized using several softwares (e.g. PyMol, LigandScout, MOE, NGLView). The dMIFs can be further processed to generate pharmacophores enabling high-throughput virtual screening.