Form handling in Flask

Now I’m coding simple design-tracking system. Almost looks like a blog service. I use Flask as web app flame work. But I’m not good at web design. It’s difficult for me to make form template. There are some extensions about Flask.  And I found that using Flask-Bootstrap( Bootstrap ) make easy to beautiful layout. KeyContinue reading “Form handling in Flask”

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ErGFingerprint in RDKit

Sometime, medicinal Chemists think about scaffold hopping approach in drug discovery project to overcome their issue. When I think about scaffold hopping, I consider about what’s key interaction of molecule and protein. It’s called pharmacophore. And also hopping approach is used me too approach to find another IP space. BTW, In 2006, researchers in LillyContinue reading “ErGFingerprint in RDKit”

Application of Fragment molecular orbital method (FMO ) against GPCR

To understand interaction of molecule and protein is important but difficult step of drug discovery. In case of SBDD, researcher often analyse structural data. But, it’s difficult to understand nonclassical interaction. FMO is one of the tool to analyse ligand-molecular interaction more deeply than MM. Today I read very impressive paper. “The Fragment Molecular OrbitalContinue reading “Application of Fragment molecular orbital method (FMO ) against GPCR”

Draw molecule as SVG Part2.

New version of rdkit can draw molecule as SVG. And newest version of it can change atom font size. I’m waiting for this function for a long time. ;-) Let’s Draw! From ipython notebook… Then I got following image. Next change font size.(default size is 0.5.) Then I got…. Cool! Nice stuff. I want toContinue reading “Draw molecule as SVG Part2.”

New fingerprint algorithm using RDKit

I often use ECFP4 for building QSAR models. Because, I think the algorithm represents details of molecules. Original circular finger print can be calculated using pipeline pilot. But, RDKit also can calculate ECFP4 like fingerprint called Morgan-Finger print. BTW, when I tried to build QSAR models using chainer, I had one question that ECFP4 reallyContinue reading “New fingerprint algorithm using RDKit”