Make simple web API with FastAPI, pycembldb and razi #chemoinformatics #RDKit #ChEMBLDB

As reader know, chembl is not only useful but also opensource database. Recently I’m playing with chembl and its python wrapper named pychembldb and cartridge named razi. I recommend reader who is interested in the chemoinformatics to install these very useful python packages. ;) BTW, I think it is useful if I could use theseContinue reading “Make simple web API with FastAPI, pycembldb and razi #chemoinformatics #RDKit #ChEMBLDB”

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Bio-isoster of Aryl amine #memo

As medicinal chemists know that aryl amine building blocks are often used in drug design. N linked Bi Aryl motif can found many kinase inhibitors but sometime aryl amine cause toxic issues so the structure is recognized as alert structure. So, there are many researches for aryl amine replacement with another structure. Here is aContinue reading “Bio-isoster of Aryl amine #memo”

Integration razi and pychembldb #RDKit #Chemoinformatics #razi #sqlalchemy #ChEMBL

As you know, sqlalchemy is very useful ORM of python. I love the package and also chemoinformatician is familiar to ChEMBLDB I think. There are very useful package for these people one is razi and the other is pychembldb. Razi is chemical cartridge for postgressql with rdkit functionality and pychembldb is python wrapper of ChEMBLDBContinue reading “Integration razi and pychembldb #RDKit #Chemoinformatics #razi #sqlalchemy #ChEMBL”

Rendering molecular image tooltips on Bokeh #RDKit #memo #visualization

Recently there many plotting tools for python package! I can’t follow everything… I mainly use seaborn and matplotlib. These tools are nice for rendering beautiful chart but if I would like to interactive plot, I need to switch plotting tools. So I started learn another tools and today I used Bokeh. (Reader already know bokeh,Continue reading “Rendering molecular image tooltips on Bokeh #RDKit #memo #visualization”

Target prediction by conformal prediction with ChEMBL data #chemoinformatics #docker #memo

Recently I’m learning conformal prediction and today I used the ready to use model for target prediction which is trained by chembl_24 (little bit old) with lightGBM. ChEMBL team provides nice package. You can get the model as docker image. URL is below.https://github.com/chembl/of_conformalAnd original article is here. https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0325-4 To use the image in your localContinue reading “Target prediction by conformal prediction with ChEMBL data #chemoinformatics #docker #memo”

Communicate ChEMBL27 with rdkit postgres cartridge and sqlalchemy #RDKit #ChEMBL #Postgres #razi

As you know ChEMBL 27 was released recently, thanks great effort for EBI ;) Fortunately ChEMBL provides common DB format dump file and RDKit has postgres DB cartridge. It means that you can search compound with rdkit functionality in postgres. BTW, to handle the database, sqlalchemy which is ORMapper is very useful. So is itContinue reading “Communicate ChEMBL27 with rdkit postgres cartridge and sqlalchemy #RDKit #ChEMBL #Postgres #razi”