Make curated Kinase inhibitor dataset from ChEMBL30 #memo #chemoinformatcs

Kinase is one of the attractive target for drug discovery. So there are lots of data not only protein but also inhibitor available. ChEMBL is useful public data source for Kinase inhibitor data however to use the data, we need to retrieve data from the DB and curate it. Of course there are commercial databaseContinue reading “Make curated Kinase inhibitor dataset from ChEMBL30 #memo #chemoinformatcs”

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Extract macro cyclic compounds from ChEMBLDB with rdkit_cartridge #chemoinformatics #RDKit

As you know, RDKit has really useful postgreSQL cartridge. So it’s easy to do substructure or similarity search of query structure from postgresql ChEMBLDB. But I don’t know how to retrieve only macrocyclic compound from ChEMBLDB with the cartridge. I searched RDKit mailing list and got good answer! Thanks for the community. This is theContinue reading “Extract macro cyclic compounds from ChEMBLDB with rdkit_cartridge #chemoinformatics #RDKit”

Modify version of RDKit/Contrib/pzc #chemoinformatics #RDKit #ChEMBL #pychembldb

In 2013, Dr. Paul Czodrowski published nice article in JCIM. And the code is available from github. And also Paul contributed rdkit with the code. https://github.com/pzc/rdkit/tree/master/Contrib/pzc This code can build model from chembl activity data set with given accession number as a query. I had interest the code however, the code is old. So itContinue reading “Modify version of RDKit/Contrib/pzc #chemoinformatics #RDKit #ChEMBL #pychembldb”

Update conda package of rdkit-postgresql #rdkit #postgresql

Yesterday, I enjoyed mishima.syk #16. Due to recent COVID-19, we moved the meeting to virtual style and worked very well. As same as RDKit UGM 2020, we used Zoom for presentation and discord for discussion and chat. Discord was very useful and easy to use. Thank for all participants and member of the community. TheContinue reading “Update conda package of rdkit-postgresql #rdkit #postgresql”

FPSim2 for fast compound search #fpsim2 #rdkit #chemoinformatics

In the previous posts, I described various way to search compounds from data source such as ChEMBL. For example… using rdkit postgre cartridge, GPUsim which is developed by schrodinger and rdSubstructLibrary which is implemented in RDKit. All methods are very useful. And today I tried to use FPSim2 which was described in ChEMBL-OG. The packageContinue reading “FPSim2 for fast compound search #fpsim2 #rdkit #chemoinformatics”

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”