Let’s update MMPDB #RDKit #mmpdb #Chemoinformatcs

Matched molecular pairs are popular approach to transform molecules with prior knowledge of medicinal chemistry. MMPDB is useful open source package for managing MMP dataset which is derived from GSK  under the 3-clause BSD license.  It is easy to use and work really fast. I love it the package. However current version of MMPDB supportsContinue reading “Let’s update MMPDB #RDKit #mmpdb #Chemoinformatcs”

Create MMPDB ( matched molecular pair )!

Matched molecular pair analysis is very common method to analyze SAR for medicinal chemists. There are lots of publications about it and applications in these area. I often use rdkit/Contrib/mmpa to make my own MMP dataset. The origin of the algorithm is described in following URL. https://www.ncbi.nlm.nih.gov/pubmed/20121045 Yesterday, good news announced by @RDKit_org. It isContinue reading “Create MMPDB ( matched molecular pair )!”

After mishima.syk #4

Thank a lot for all attendance and presenters at mishima.syk #4 ! I enjoyed the event and party. All presentations were very interesting and exciting. ;-) I made brief introduction about cytoscape.js, and up loaded my slide and sample code to slide share and git hub. slide link code link My sample apps will needContinue reading “After mishima.syk #4”

MMP using predict

I’m still thinking about how to use mmp data in our lab. Inspired following nice presentation, I challenged to make predictive model from MMPA. One of ipython notebook about rdkit. link And another is Greg’s nice presentation about reaction finger print . link2 To make predictive model from mmps, I think, I need to convertContinue reading “MMP using predict”