Run Autodock Vina on Batch mode #Vina #memo

As most of readers know that autodock vina is one of the famous open source docking tool. So users can run virtual screening on theire own PC ;) If there are many ligands to dock, some code is required to run the dock, for example following shell script is provided from original site. https://vina.scripps.edu/manual/#screening The

Run virtual screening with only python! #chemoinformatics #SBDD

If you have protein-ligand co- crystal structure at the early stage of drug discovery, SBDD based approach is useful I think. As many readers know that there are lots of useful commercial packages to conduct SBDD. But also there are useful packages at Open science area. One of the famous and useful OSS for SBDD

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 I

Self docking study workflow with vina #chemoinformatics #vina #RDKit #pdb-tools

I posted about how to run vina from python. But I split receptor and ligand with pymol GUI at previous post, Hmm…. it’s not automated process. I tried to write code for full auto self docking with vina. It will work only very limited option and case but It’ll be first step for Virtual screening

Run docking study from python #chemoinformatics #vina #RDKit

Docking is one of the popular approach for computer aided drug design. There are lots of applications to run docking not only commercial software but also open source. AutoDock Vina is one of the popular OSS for docking study and it was updated recently. The publication is below. https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c00203 Vina has python binding and it