redmine and rdkit

To think about DMTA cycle in drug discovery process, I think most important thing is ‘why you make the compound ‘. We make hypothesis to solve problems, and think about priority what make first. And make it. Next analyse assay data, and make next plan…… So, issue tracking system is good tool for hypothesis driven

GA with python

Genetic algorithm is sometime used for designing diversity compounds library set or optimising hyper parameter about QSAR etc…. I knew only one library about genetic algorithm in python ‘pyevolve’. Some days ago, I found another library deap. Development is active. I wrote sample to solve knapsack problem. Deap is installed by using pip or easy_install.

View SDF using open source toolkit.

There are lots of commercial tools to visualize structures from SDF files. Also I often use Spotfire, etc in my lab, but not use in my house. In 2014RDKit-UGM open source SDF viewing tool was presented. Today I installed it and used. If reader who interested this tool, there is nice presentation in following link.

Cloud Computing in Drug Discovery.

Recently, we can get more and more data in very short time. So, medicinal chemist need to analyse data set more rapidly and decide that what make next. I think CADD is one of the answer to solve the problem. But to analyse big data, we need much more time and resource… Today, I read