QSAR with chainer.

I wrote blog post about DL before. https://iwatobipen.wordpress.com/2014/07/07/deep-learning-with-python/ I used nolearn for QSAR in the post. There are some python library for DL. You know… Theano, nolearn, pylearn2, etc.. And chainer is new python library for neural networks. If reader interested the library, please search chainer in google, you will find lots of site or

Array or sparse array ?

In a process of lead optimization, chemist often do SAR expansion around potent compound. If lead compound can be break down three parts A(head), B(core), C(tail), chemist(me…) often fix one part(e.g core B) and change two parts. After optimize A and C then, fix A, C and change B. This approach is called array synthesis

Visualizing the process of lead optimization

Some time we set milestones to management of portfolio, or/and to check the progeress of projects. These data were reported document, power point slides etc, so it’s difficult to grasp situation of LO timely. Researchers at GSK published a solution of visualize LO process. It was impressive for me. Link is here. http://www.ncbi.nlm.nih.gov/pubmed/26262898 They called

Draw Molecular Matched Pair as SVG.

Somedays ago, I posted drawing molecule as SVG using RDKit. It works fine. So, I challenged draw MMP as SVG. My plan is … 1. Generate MMP using RDKit. 2. Store MMP data to MongoDB. 3. Provide MMP data to user using flask. 4. Draw structure on the fly using Ajax. OK, Let start! Step