calculate fingerprint

I’m interested in chemoinformatics and machine learning and a fun of RDKit. (But I’m still …..) Calculate molecular fingerprint is a very important process to build QSAR model. I some time use RDKit-Morgan Fingerprint (like scitegic ECFP4). Chemfp is a good tool to calculate many type of fingerprint . It can generate and search fingerprintContinue reading “calculate fingerprint”


sqlalchemy and PANDAS

PANDAS is high-performance, easy-to-use data structures and data analysis tools for the Python. I love it. And Sqlalchemy is the Python SQL toolkit and Object Relational Mapper. I’m not good at SQL… ;-(, Sqlalchemy is very helpful for me. I want to make table from pandas dataframe in postgresql. I found cool method. “DataFrame.to_sql” ExampleContinue reading “sqlalchemy and PANDAS”

fisheye “GYOGAN”?

I’m newbei of javascript. There are lots of libraries. And I’m interested in D3.js. D3.js is a JavaScript library for manipulating documents based on data, and lots of plug-ins are. Today I made simple scatter plot with fisheye. Fisheye.js is plug-in of D3.js and it can distortion magnifies the local region around the mouse, OKContinue reading “fisheye “GYOGAN”?”

access CHEMBL DB with python

CHEMBL is a one of big public database. It has lots of useful data. If you are good at python, pychembldb will be good tool. I like the python package. And I found another package chembl “chembl_web_client”. The package can install using pip. Yah, it easy. OK Let’s get data from python ! For exampleContinue reading “access CHEMBL DB with python”

MPO about drug discovery

I have question about MPO multi-parameter optimisation in drug discovery. My opinion is that designed molecule’s biological activity and ADMET profile are not always correlate. So, to design molecules that has good profile, I think it is important to get data about molecules not only biological activity but also phys-chem and ADMET profile even ifContinue reading “MPO about drug discovery”