Try to use target DB #OSS #targetDB #memo

I posted the article about CADD for drug discovery today. And in the article, author introduced many useful CADD tools and targetDB is one of them.

Reader who would like to install it, pip or conda command is available.
https://github.com/sdecesco/targetDB

pip install targetdb
#or
conda install -c bioconda targetdb

I installed targetdb with pip because conda caused error during the instllation.

After installing the package I got dataset from original repository.

$ mkdir targetdbtest
$ cd targetdbtest
$ mkdir outputlists
$ mkdir outputsingle
$ wget https://github.com/sdecesco/targetDB/releases/download/v1.3.1/TargetDB_20_12_19.db.zip
$ unzip TargetDB_20_12_19.db.zip

This database contains all of the human genome genes that have a uniprot ID. Then launch service, it’s easy just type ‘targetDB’.

Tkinter app will be launched and then set db to extracted database and set folder where I made above.

After the setting I could use the app. I entered BRAF in the target list box and push the start button as single mode.

After the job finished, I could get xlsx file in the outputsingle folder.

Open the file with openoffice, I could see many information about the target. The front tab shows summary of the target.

And there are many useful tabs not only disease related information but also compound information. I pasted some screenshots of the example task.

Excel format is chemist friendly and also if user can pandas, user can extract compound data and manipulate them with rdkit or any other chemoinformatics tools.

I would like to dive more deep in the package during the week. TargetDB is useful and easy to use for me. Thanks for developing and sharing the nice package on github!

Advertisement

Published by iwatobipen

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

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: