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 can not only run docking study but also do some chemoiformatics task on python. However I couldn’t provide code for how to handle docking score….

Recently I found and read exciting article in chemrxiv published from researchers in AstraZeneca(AZ). The url is below.

https://chemrxiv.org/engage/chemrxiv/article-details/6107fc3340c8bd01539a36f4

They are really productive in this field and they shares their code. I respect their work. They developed docking study workflow named ‘DockStream’. Fortunately it’s freely available from following URL. https://github.com/MolecularAI/DockStream

The interesting point of DockStream for me is that it supports not only commercial package but also open source docking package. So I can run it in my private PC! It sounds nice doesn’t it.

So I tried to use it in my environment today. As same as REINVET, they shared DockStreamCommunity where provides some example code for running dockstream. It’s really helpful to run the code. OK, let’s write code and run it ;) At first I made DockStream environment.

gh repo clone MolecularAI/DockStream
cd DockStream
conda env create -f environment.yml
conda activate DockStream

I use AutoDock vina and RDKit for this example because don’t have private OpenEye and Schrodinger licence.

Most of code for making configuration file was borrowed from DockStreamCommunity. And here is a my test code. I modified input_pools parameter from OE based module to RDKit. It means that the process will generate conformer with RDKit.

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After running the code, I could get results with score. This will be useful for data analysis.

(chemoinfo) iwatobipen@penguin:~/Desktop/AutoDock_Vina_demo$ cat ADV_scores.csv 
ligand_number,enumeration,conformer_number,name,score,smiles,lowest_conformer
0,0,0,0:0:0,-9.2,C#CCCCn1c(Cc2cc(OC)c(OC)c(OC)c2Cl)nc2c(N)ncnc21,True
0,0,1,0:0:1,-8.3,C#CCCCn1c(Cc2cc(OC)c(OC)c(OC)c2Cl)nc2c(N)ncnc21,False
1,0,0,1:0:0,-9.0,CCCCn1c(Cc2cc(OC)c(OC)c(OC)c2)nc2c(N)ncnc21,True
1,0,1,1:0:1,-8.9,CCCCn1c(Cc2cc(OC)c(OC)c(OC)c2)nc2c(N)ncnc21,False
2,0,0,2:0:0,-9.1,CCCCn1c(Cc2cc(OC)ccc2OC)nc2c(N)ncnc21,True
2,0,1,2:0:1,-8.2,CCCCn1c(Cc2cc(OC)ccc2OC)nc2c(N)ncnc21,False
3,0,0,3:0:0,-9.2,CCCCn1c(Cc2cccc(OC)c2)nc2c(N)ncnc21,True
3,0,1,3:0:1,-8.2,CCCCn1c(Cc2cccc(OC)c2)nc2c(N)ncnc21,False

The target protein is Human Hsp90(1UYD) as same as original code. It is surprising for me that recently it’s easy to run docking study at home.

I really appreciate the great work. Thanks.

Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

3 thoughts on “New tool for automatic docking simulation with python #chemoinformatics #CADD #rdkit #vina

  1. Thank you so much for your blog.
    From your notebook, I couldn’t find how docking and reinvent are coupled together? I don’t know how to Using DockStream as a scoring component in REINVENT. Do I need to go to the Reinvent virtual environment? Many thanks

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