Tag Archives: chemoinfomarics

Run Knime workflow without GUI #chemoinfo #knime #RDKit

I enjoyed knime summit last week. I could learn lots of useful features of new version of Knime (ver5). Knime is useful tool for chemoinformatics but I mainly write code with python so I’m not heavy user of knime but recently I’m interested in Knime and learning to apply it in my projects. As readerContinue reading “Run Knime workflow without GUI #chemoinfo #knime #RDKit”

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”

Update announcement of shape-it #chemoinformatics #RDKit #shape-it

The end of the last year, I tried to update shape-it and shared my code on github. My new version of shape-it could supports openbabel3.xhttps://github.com/iwatobipen/shape-it-ob3 After that, I got really wonderful offer from @dr_greg_landrum. He modified the code which uses RDKit instead of Openbabel and be used as library instead of command line tool. It’sContinue reading “Update announcement of shape-it #chemoinformatics #RDKit #shape-it”

Lilly’s Chemoinformatics Tool Kit #memo #chemoinformatics

Almost 7 years ago, I posted a topics about Lilly’s MedChem filter which is disclosed on github. https://iwatobipen.wordpress.com/2013/08/06/lilly%E3%81%AE%E3%83%95%E3%82%A3%E3%83%AB%E3%82%BF/ It’s interesting for me because most of languages of code on Lilly’s repository are not python and C++, R etc. And one of interesting code is LillyMol. The licence of the code is Apache 2.0. I feltContinue reading “Lilly’s Chemoinformatics Tool Kit #memo #chemoinformatics”

Visualize atom weight of AttentiveFP #DGL #RDKit #Chemoinformatics

Yesterday, I posted an example of DGL (almost same as original example code). And I could make regression model with my own dataset. Fortunately DGL developer provides a code for visualize atom weights of trained model. It means that, after building the model with AttentiveFP, you can visualize atom weight of the give molecule whichContinue reading “Visualize atom weight of AttentiveFP #DGL #RDKit #Chemoinformatics”