Draw RDKit mol/reaction object on HTML without static png image #RDKit #memo

I think this post might not useful for many people. Just for my memorandum. When I make web app, I use draw SVG function for rdkit object rendering. But from last my post and Greg’s gist, I could learn draw png image without writing static png files. So I wonder that can I draw PNGContinue reading “Draw RDKit mol/reaction object on HTML without static png image #RDKit #memo”


Edit reaction image and draw it #RDKit #memo

I often use rdkit on jupyter notebook because notebook can render molecules very conveniently. However I couldn’t find way to edit font size of reaction some days ago. Following code is an example. Changing atom font size of MolToImage is easy but reaction image can’t apply same manner. OK, next tried to change font size.Continue reading “Edit reaction image and draw it #RDKit #memo”

Process development of fluorinated-pyrrolidin analogue #memo #organic_chemistry

Here is an interesting article for efficient synthesis of fluorinated pyrrolidin synthesis from pfizer.https://pubs.acs.org/doi/abs/10.1021/acs.oprd.9b00245 Fluorine containing building blocks are often used medicinal chemistry. So efficient synthetic route is very useful for us. Some years ago, I synthesized similar compounds 1-fluoro-2-amino cyclic amine derivatives. I tried to use almost same synthetic scheme described in scheme1. 1)Continue reading “Process development of fluorinated-pyrrolidin analogue #memo #organic_chemistry”

New fluolination reaction from JACS #memo #organicchemistry

Trifuloromethylation is useful reaction in drug discovery. Because CF3 and other fluorinated substituent are often used in drug like molecules. It is also useful that the reaction can conduct in asymmetric manner. I read interesting article in JACS today published by Trost’s group. The URL of the article is below.https://pubs.acs.org/doi/10.1021/jacs.9b06231 You can see abstract withoutContinue reading “New fluolination reaction from JACS #memo #organicchemistry”

Virtual Screening(VS) with over hundred million compound in a few days! #Chemoinformatics

Recently virtual screening often is used for first screening for drug discovery project. Because it can screen huge amount of compound very fast compared to wet screening. I thought docking score is not reflect binding affinity of ligand and target protein. But today I read interesting article and I changed my mind.The title was ‘Ultra-largeContinue reading “Virtual Screening(VS) with over hundred million compound in a few days! #Chemoinformatics”