Andrea Zaliani, Jörg Degen, and Matthias Rarey

Due to the amount of techniques/programs used, there is a growing need in the medicinal chemistry community to define and deliver validation studies aimed at benchmarking the current "state of art". A noticeable amount of work has been recently published in the field of virtual screening for what concerns, for instance, flexible docking techniques and similarity search methods. For some techniques, like structure-based de novo design, comprehensive retrospective validation work has still to be published. This particular design technique is emerging as a viable source of computer-aided designed molecules. However, it has not yet delivered a large and comprehensive evidences of its generality and efficacy. Here we would like to propose a standard approach for the validation of this particular technique. We propose a standardization of retrospective validation studies. In doing so, we show how FlexNovo, a recently introduced program, behaved. We define requirements for strict validation cases and propose suggestions for real-life cases, where it is difficult to judge the quality of the molecules obtained. First, the software should be capable to reproduce known ligands in, second, the same binding mode as presented by experimental structural data taken as reference. This latter requirement should be preferentially accomplished by ranking the candidate within the first five or ten entries of the final list. High ranking is more a preference than a strict requirement as it is usually strictly dependent on the reliability of scoring function in measuring binding energy contributions. Beside this, we also identified a third requirement for those cases where successfull prospective studies are presented. A denovo design software should be able to propose candidate molecules, which can be actually made and be stable enough to be chemical-physically characterized and tested. We presented here the results of a retrospective validation study which follows the above mentioned requirements