Attentive FP with DGL-LifeSci #RDKit #DGL #Chemoinformatics

I posted some code about DGL before. Recently DGL team published life science focused package DGL life sci. It seems almost as same as DGL but code is well organized. User can install the package from conda! And I got some comments about my attentive FP example. So I tried to use new DGL-LS andContinue reading “Attentive FP with DGL-LifeSci #RDKit #DGL #Chemoinformatics”

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Ultra fast similarity search with GPU #RDKit #chemoinformatics #postgresql-rdkit

Recently chemoinformatician need to tackle against huge amount of molecules. Search similar molecules from millions of compound database. Last year, schrodinger which is computer science company disclosed useful code for fast compound search module named gpusimilarity. You can get details of the module from schrodingers github repository. URL is below.https://github.com/schrodinger/gpusimilarity/blob/master/gpusimilarity_rdkit_presentation.pdf The algorithm is implemented inContinue reading “Ultra fast similarity search with GPU #RDKit #chemoinformatics #postgresql-rdkit”

Computer Aided Synthetic Planning in Pharma #Chemoinformatics #memo

Some days ago, I had interesting discussion about CASP in twitter and today I found good article about CASP. Here is an exciting article about current status of AI in medchem synthesis published from MLPDS consortium. https://pubs.acs.org/doi/pdf/10.1021/acs.jmedchem.9b02120 Fortunately the article can be accessed freely thanks for author’s kindness. The article describes the potential and limitationsofContinue reading “Computer Aided Synthetic Planning in Pharma #Chemoinformatics #memo”

One liner command tool for LillyMedChemRules #Chemoinformatics #memo

There are many substructure files are available in these days. And LillyMedChem Rules is one of useful and famous filter. It works very fast and provides reasonable results. However the implementation returns the result as multiple files. So user need to marge files after filtration. So I wrote small script to conduct filter the moleculesContinue reading “One liner command tool for LillyMedChemRules #Chemoinformatics #memo”

Article abut MMPA for drug design #memo #chemoinformatics

I love ‘Journal of chemoinformatcs’ because it is free access paper and has lots of useful and exciting articles. So I can access the journal from my personal computer. Thanks for maintainer! Today I read interesting article ‘Predicting liver cytosol stability of smallmolecules’. Predicting metabolic stability is very useful and important task for drug discovery.Continue reading “Article abut MMPA for drug design #memo #chemoinformatics”