Flexsim-X: a method for the detection of molecules with similar biological activity

We describe the development of the method Flexsim-X, which can be used to detect molecules with similar biological activity. This procedure is based on comparing virtual affinity fingerprints made up from docking scores of the molecules with respect to a reference set of binding sites. Using a test data set consisting of ligands from five different activity classes and randomly chosen compounds, the reference panel of binding sites was optimized in terms of size and composition. Systematic approaches as well as genetic algorithm based (GA) optimization procedures have been evaluated. Additionally, the effectiveness of the method is illustrated.