SAR visualization with RDKit ver2.

Somedays ago I posted SARviz test code using RDKit. It was based on command line type. So, I think it is easy to use for applying SDF etc but not familiar for chemist. Because almost of chemist, don’t like black command screen….;-) Next step, I tried to make very simple web-app using sarviz.py. I used

Call CDK from Python

Somedays ago, I wanted to use molecular signature descriptors. But the descriptor can’t calculate from RDKit. ref. http://pubs.acs.org/doi/abs/10.1021/ci020345w It was implemented in CDK. Hmm, CDK,,, Java library, I’m not good at JAVA :-/. I found old, but good information from CDK news and noel’s blog! URL is following https://www.redbrick.dcu.ie/~noel/CDKJython.html Jython is one of solution. I

SAR visualization with RDKit.

I’m interested in machine learning(ML) for QSAR. RandomForest, Neural Network, SVM etc. are often useful tool for drug design. But it difficult to interpretation of results for chemist. So, visualization / interpretation of SAR is critical for communication. You know, Prof. J. Bajorath reported very nice solution of the problem. http://www.ncbi.nlm.nih.gov/pubmed/25988274 The article was impressive

JP-Clustering with python and rdkit.

Some days ago, my colleague asked me how to do jarvis-patrick clustering using python. JP-clustering is one of unsupervised learning method. It’s almost like k-mean clustering. I found good solution for answering his question. A library named “jarvispatrick” was developed recently and uploaded to pypi. ;-) So, the library can be installed using pip command.

New python library for chemoinformatics using RDKit.

Last sunday, I read an article of J. Chem. Informatics. The title was “Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets”. URL is following http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0125-7 The author developed python library that analyse relation ship between structure and tox / bioactivity. Sometime I use machine-learning or knowledge based

ChemblDB 21 was released!

Some days ago, CHEMBLDB 21 was released. I installed chembldb 21 to my mac book yesterday. (postgres.) I checked DB schema and interested in some table. New chembl has table about metabolism. ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_21/chembl_21_schema_documentation.htmlt has data about drug metabolism pathways. I checked db. Type SQL query. I used copy command to get data as CSV format.

Business trip

I’m visiting some foreign CROs. They have good facilities and scientists. And the most impressive point of my trip was that a lots of scientists are really enjoying science! ;-) And they work really systematic. Lots of parts of drug discovery project can do by outsourcing in these days. So, I’m rethinking about role of MedChem.