Matched Molecular Pair Analysis in Short: Algorithms, Applications and Limitations

Abstract Molecular matched pair (MMP) analysis has been used for more than 40 years within molecular design and is still an important tool to analyse potency data and other compound properties. The methods used to find matched pairs range from manual inspection, through supervised methods to unsupervised methods, which are able to find previously unknown molecular pairs. Recent publications demonstrate the value of automatic MMP analysis of publicly available bioactivity databases. The MMP concept has its limitations, but because of its easy to use and intuitive nature, it will remain one of the most important tools in the toolbox of many drug designers.