Comments on the design of chemical libraries for screening

Different representations of molecules, based ondistinct sets of properties can yield differentperspectives of the issues involved in library design.In particular, different chemical representations cangive rise to very different estimates of requiredlibrary sizes. We provide a preliminary mathematicalframework that examines the size of libraries requiredto adequately sample the spaces corresponding to somecommonly used property sets. Introduction ofconformational flexibility is also discussed as ameans of increasing coverage of chemical libraries,while at the same time considering the thermodynamicconsequences of flexibility upon detectable activity.Our theoretical analysis reveals that the propertyspaces currently in use are extremely large andunlikely to provide adequate discrimination amongcompounds.