An experiment with MorganFP #RDKit #chemoinformatics

Tokyo Olympic opening ceremony is coming. I hope the Olympic will be safe and secure. Today I tested to compare fingerprints from molecule and fragments. Because if I can construct the identical fingerprint from fragments, it’s useful. Following code is very simple example used 1,3 and 1,2 di-substituted benzene. I calculated fingerprint of each moleculeContinue reading “An experiment with MorganFP #RDKit #chemoinformatics”


Data analysis of MMP “from OR to Fluorine” #memo #journal

Control lipophilicity is key strategy for drug design. Medicinal chemist often struggle to ADMET issue due to their compound lipophilicity. Sometime ADMET issue can be improved by reducing LogD but it cause loss of potency. Matched molecular pair approach is used to find bioisosteric replacements that mean the substructure replacement with keeping potency but changeContinue reading “Data analysis of MMP “from OR to Fluorine” #memo #journal”

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”