Run MD simulation with cloud resource #openmm #google_colab

Molecular dynamics (MD) simulation is one of the useful approach for estimating protein-ligand interaction. However, computational cost of MD simulation is high, so large computational resource is required when we run the large scale MD simulation. On the other hand, now we can use freely available could computational resource such as Google colab. It’s notContinue reading “Run MD simulation with cloud resource #openmm #google_colab”


Reinforcement learning with docking score #RDKit #reinvent #chemoinforamtics

Previously I posted automated docking system called dockstream. It supports many compound-protein docking software and recent version of reinvent supports dockstream as scoring method. From the dockstream documentation, reinvent v3.0 supports dockstream but it didn’t work due to some issue of reinvent-scoring which manage scoring function of reinvent. I modified source code to use dockdreamContinue reading “Reinforcement learning with docking score #RDKit #reinvent #chemoinforamtics”