PathGennie

Category: Science & Technology / Computational Biology

  • PathGennie is a computational toolkit designed for rapid generation of rare-event molecular pathways.
  • It uses direction-guided adaptive molecular-dynamics sampling.
  • It can work with molecular-dynamics backends such as AMBER, GROMACS and OpenMM.
  • Applications include studying processes such as ligand unbinding, protein folding/unfolding and conformational changes.
  • It can use data-driven collective variables and adaptive sampling to identify possible molecular pathways.
  • It is relevant to computational chemistry, molecular simulation and drug-discovery research.

Prelims Pointers: Field → Molecular simulation | Method → Adaptive MD sampling | Applications → Protein folding + ligand unbinding.