Visualize MMP data with OSS webapp! #chemoinformatics #rdkit #mmpdb

Matched molecular pairs (MMPs) are old but still useful approach for not only retrospective analysis but also forward compound design. As many chemoinformatitians know that mmpdb is the one of famous MMP CLI tool. I like tha package because it’s easy to make own MMP db. However mmpdb doesn’t have visualization tool for chemists. SoContinue reading “Visualize MMP data with OSS webapp! #chemoinformatics #rdkit #mmpdb”

Use mmpdblib on jupyter notebook #rdkit #mmpdb #chemoinformatics

I introduced MMPDB v3 few days ago. The package is CLI tool. So user can do MMPA by typing command line. However the tool doesn’t provide API interface. I think, if we can use MMPDB on jupyter-notebook it’ll be more useful because output data can be used directly in coding process. MMPDB Cli interface isContinue reading “Use mmpdblib on jupyter notebook #rdkit #mmpdb #chemoinformatics”

Let’s use mmpdb v3 #memo #rdkit #chemoinformatics

Matched molecular pair (MMP) is not AI based compound design method however it’s still useful and powerful approach to do compound design. MMPDB is one of the cool package for MMP analysis. And Andrew who is developer of MMPDB preseted new version of MMPDB at RDKit UGM 2022. Version 3 is still developing state butContinue reading “Let’s use mmpdb v3 #memo #rdkit #chemoinformatics”

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. 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”