demos

molecular docking demo

This notebook demonstrates how to dock a ligand to a protein. As an illustrative case, I used cocaine docking to the human dopamine transporter. The workflow relies on an open‑source docking package.

ligand-based method

• Machine learning-based QSAR modeling for DAT-hERG
  The results are published in JCIM: 'Toward Reducing hERG Affinities for DAT Inhibitors with a Combined Machine Learning and Molecular Modeling Approach'. In the DAT-hERG repository, our initial instructions were built here, and now we have expanded its functionality further. These additions are not in the public domain.

structure-based method

Strucutral anaylses and MD simulation for aminergric family GPCR

• aminergic_receptors_2023-03
  The results are published in JCIM: 'A novel “activation switch” motif common to all aminergic receptors'.

• dopamine_D2_D3_receptors_2023-03
  The results are published in JCIM: 'Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors'.