Lemon

Lemon' is a software tool designed to facilitate benchmarking of virtual screening methods for drug discovery. It addresses the challenge of having different formats for representing protein and ligand structures used in benchmarking. The Directory of Useful Benchmarking Sets (DUBS) framework introduced by Lemon' provides a simple and flexible way to create benchmarking sets using the protein databank. DUBS uses a simple input text-based format and the Lemon data mining framework to efficiently access and organize data. This allows users to define their own benchmarking datasets and access them directly from the software package. With DUBS, creating a benchmark takes only about 2 minutes, making it an efficient tool for virtual screening. Its simplicity also makes it easy for users to modify and create more complex benchmarks. Overall, DUBS aims to provide a standardized representation for benchmarking datasets in virtual screening, which can help improve the evaluation of virtual screening methods.