Method of selecting marker molecules for prediction of molecular activity

A computer-implemented method of selecting marker molecules that are for constructing a model for predicting whether a test molecule has a chemical or biological property of interest using said marker molecules that are known to possess said chemical or biological property of interest, said method comprising:

• classifying respective molecules in a training set of reference molecules as either possessing or not possessing said chemical or biological property of interest, wherein said classifying is based on experimental data;
• selecting, from said training set, a plurality of molecules that possess the chemical or biological property of interest as target molecules for potential selection as marker molecules for said model;
• selecting some of said target molecules as marker molecules for said model by evaluating the predictive accuracy of said potential marker molecules, wherein said evaluating comprises:
• computing a numerical value defining a measure of molecular structural similarity for each pair of molecules in said training set using a pre-defined structural similarity metric;
• selecting one of said target molecules (T);
• sorting all training set molecules in descending order of structural similarity to molecule T as defined by the computed numerical values;
• defining, for a first one of said sorted training set molecules (M) a fractions-correctly-predicted metric as a ratio of A/B, wherein B is defined as the total number of training set molecules that have a computed numerical structural similarity to molecule T that is as large or larger than the computed numerical structural similarity between molecules T and M, and wherein A is defined as the number of training set molecules that both (1) have a computed numerical structural similarity with molecule T that is as large or larger than the computed numerical structural similarity between molecules T and M, and (2) possess the chemical or biological property of interest;
• repeating the defining step for other sorted training set molecules;
• choosing molecule T as a marker molecule if said number B and said ratio A/B are both above respective threshold values when computed during at least one of said defining steps;
• and
• outputting data indicating that molecule T has been chosen as a marker molecule.