Matched molecular pair analysis (MMPA) is a popular structure activity method in cheminformatics that compares the properties of two molecules that differ only by a single chemical transformation, (e.g. substitution of a hydrogen atom by a chlorine atom). Because the structural difference between the two molecules is small, any experimentally observed change in a physical or biological property between the matched molecular pair could be associated with this particular molecular transformation.

Andrew Dalke has recently published open source code to support this methodology https://github.com/adalke/mmpdb/tree/v3-dev.

To install

python -m pip install mmpdb

The package has been tested on Python 3.9.

You will need a copy of the RDKit cheminformatics toolkit, available from http://rdkit.org/ , which in turn requires NumPy. You will also need SciPy, peewee, and click. The latter three are listed as dependencies in setup.cfg and should be installed automatically.

Full details are described in this publication.

A. Dalke, J. Hert, C. Kramer. mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets. J. Chem. Inf. Model., 2018, 58 (5), pp 902–910. DOI.