Make predictive models with small data and visualize it #Chemoinformatics

I enjoyed chemoinformatics conference held in Kumamoto in this week. The first day of the conference, I could hear about very interesting lecture. That was very basic data handling and visualization tutorial but useful for newbie of chemoinformatics. I would like to reproduce the code example, so I tried it. First, visualize training data. It

standardization of tautomers #RDKit

One of the hot topic of new version of RDKit is an integration of MolVS which is tool for molecular standardization. Molecular standardization is important for not only chemist but also chemoinformatist. Because tautomer shows different representation of molecule and it will be affect accuracy of QSAR models. I wrote molecular standardization tools named ‘MolVS’

New finger print calculation method in RDKit #RDKit

It’s a good news for RDKitters! New version of rdkit is released and it can be installed with Anaconda! There are many implementations and enhancements. You can find details of that from URL below. https://github.com/rdkit/rdkit/blob/master/ReleaseNotes.md One of interesting feature is a fingerprint bit information rendering function. There is nice blog post about that. http://rdkit.blogspot.com/2018/10/using-new-fingerprint-bit-rendering-code.html And

(new?) medchem tool box for compound synthesis

This mini perspective shows recent progress of the direct C-H alkylation with Alkyl Sulfinates. https://pubs.acs.org/doi/10.1021/acs.jmedchem.8b01303 There are many heterocyclic moieties such as pyridine, pyrrole etc. in drug like molecules. The C-H alkylation reaction of heterocycles is useful but difficult to conduct it under mild reaction conditions. So mild and universal reaction is very attractive for

Draw similarity network #RDKit #Cyjupyter

Recently Kei Ono who is developer of cytoscape developed cyjupyter. https://pypi.org/project/cyjupyter/0.2.0/ It seems attractive for me because the library can draw network diagram on jupyter notebook. There are many network structured data in chemoinformatics. For example molecule, molecular similarity map and MMP etc… I used the library to draw similarity map of molecules today. I

New fingerprint/MinHash FingerPrint #RDKit #Chemoinformatics

Recently I found an article that describe new method for fast fingerprint calculation. You can read the article from chemrxiv, URL is below. https://chemrxiv.org/articles/A_Probabilistic_Molecular_Fingerprint_for_Big_Data_Settings/7176350 They used MinHash method. MinHash method is the way to estimate jaccard similarity very efficiently. The authors developed MHFP (MinHash Fingerprint) and compared the performance with ECFP4. ”’ ? MinHash ?

Diary….

I like my town. This town is comfortable for me to live in, because it is not too urban like Tokyo or rural. There are many beautiful place and following pictures are my favorite place.  The water in this river is very clean. I can see firefly in summer around here. I want to  this scenery