Generate conformers script with rdkit #RDKit #Chemoinformatics

As you know, conformer sampling is an important task for not only SBDD but also LBDD because many drug like molecules has rotatable bonds so, they has possibility to have many conformations. And recently there are lots of tools for compound conformer generation. Jean-Paul Ebejer et al. published very useful article about conformer generation withContinue reading “Generate conformers script with rdkit #RDKit #Chemoinformatics”

Rationalize of none additive SAR #memo #journal

In medicinal chemistry, chemists often make compound analogue which differ only a part. Optimization of R1, R2 etc… After optimized each R group, combination strategy is tried because it is expected that combination make additive effect for potency. But sometime combination strategy doesn’t work well. To understanding the phenomenon structural information is important. And recentlyContinue reading “Rationalize of none additive SAR #memo #journal”

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.x 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”

Handle rdkit molobjects with String/BytesIO #RDKit #memo

This post has no new topics but just for my memo. I often want to read and write molecule ad hoc without writing them to file objects. RDKit has two kinds of SDF reader one is SDMolSupplier and the other is ForwardSDMolSupplier and has a SDF writer SDWriter. SDWriter supports StringIO and Forward SDSupplier supportsContinue reading “Handle rdkit molobjects with String/BytesIO #RDKit #memo”

Chemical structure generation without GPU #chemoinformatics #STONED #rdkit

Generative model is very hot not only in computer vision, natural language processing but also chemoinformatics. As you know, recent version of deep learning based compound generator works very well but it is required huge computer resources for building the model. And also SMILES based approach sometime generates invalid molecules. Recently I read very interestingContinue reading “Chemical structure generation without GPU #chemoinformatics #STONED #rdkit”

Python package for Automated Graph Learning #DeepLearning #GraphLearning #Chemoinformatics

I hope you have great start of 2021! This is my first post of new year! For there are many data which can be represented as graph. So graph based deep learning(GL) is very interesting area. In chemistry area, molecule can be represented as graph so GL is also attractive method for chemoinformatics. I postedContinue reading “Python package for Automated Graph Learning #DeepLearning #GraphLearning #Chemoinformatics”