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 is

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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 but

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 supports

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 is

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 need

Get min and max values.

I made some web apps in our lab. I want to make mmp app. For make it, I need function that can set range like spotfire. HTML5 range tag is not enough. …. I found good JS library noUiSlier ! It’s easy to get min and max value from slid-bar. I wrote code using flask.

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 convert