Methods for predicting an active set of compounds having alternative cores, and drug discovery methods involving the same

Abstract

A system, device, and method for predicting an active set of compounds that bind to a biomolecular target is disclosed. The system and device contain modules allowing for the prediction of an active set of compounds. A core identification module can identify the core of an initial lead compound. A core hopping module is used to identify potential lead compounds having different cores compared to the core of an initial lead compound. A scoring module can use computational techniques to calculate the relative binding free energy of each identified potential lead compound. An activity prediction module can use the relative binding free energy calculations to predict an active set of compounds that bind to the biomolecular target. Empirical analysis can be used to inform the accuracy and completeness of the predicted active set of compounds.