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”

New tool for automatic docking simulation with python #chemoinformatics #CADD #rdkit #vina

After my surgery, I could run 16km today at the first time ;) The pace was slow but I felt that I’m getting well. So I could spend nice week end… Ah, let’s back to chemoinforamtics topic. Previously, I posted how to run docking study with autodock-vina via python. I think it’s interesting because IContinue reading “New tool for automatic docking simulation with python #chemoinformatics #CADD #rdkit #vina”

Cross docking study with python #Vina #Pymol #RDKit

I hope reader doing well and having nice weekend. Due to COVID-19 pandemic, our life is dramatically changed. I would like to go camp with my family when the pandemic is over. Last month, I wrote post about self docking (how to prepare input file and run vina from python) with vina-python API. Today IContinue reading “Cross docking study with python #Vina #Pymol #RDKit”