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 screeningContinue reading “Self docking study workflow with vina #chemoinformatics #vina #RDKit #pdb-tools”

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Memo from ACS medicinal chemistry letters #memo #journal

Recently I spend most of my working time at my desk because I’m member of chemoinformatics team. When I worked at bench as a chemist, I often used not only LCMS but also TLC for checking reaction progress. UV lump is common tool for visualizing spot if reagents has uv reactive substituents such as phenylContinue reading “Memo from ACS medicinal chemistry letters #memo #journal”

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 itContinue reading “Run docking study from python #chemoinformatics #vina #RDKit”

Get environment SMILES around cutting points #chemoinformatics #memo #RDKit

In this week, I’m in summer vacation but can’t go travel due to COVID19 pandemic and heavy rain. It’s really unusual summer vacation. I hope everyone stay safe. BTW, I often use R-Group decomposition and Matched molecular pairs and these method generate many fragment smiles which has [*] at attachment points. And I would likeContinue reading “Get environment SMILES around cutting points #chemoinformatics #memo #RDKit”