DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening.

Benchmarking is a crucial step in evaluating virtual screening methods for drug discovery. One major issue that arises among benchmarking data sets is a lack of a standardized format for representing the protein and ligand structures used to benchmark the virtual screening method. To address this, we introduce the Directory of Useful Benchmarking Sets (DUBS) framework, as a simple and flexible tool to rapidly create benchmarking sets using the protein databank. DUBS uses a simple input text based format along with the Lemon data mining framework to efficiently access and organize data to the protein databank and output commonly used inputs for virtual screening software. The simple input format used by DUBS allows users to define their own benchmarking data sets and access the corresponding information directly from the software package. Currently, it only takes DUBS less than 2 min to create a benchmark using this format. Since DUBS uses a simple python script, users can easily modify this to create more complex benchmarks. We hope that DUBS will be a useful community resource to provide a standardized representation for benchmarking data sets in virtual screening. The DUBS package is available on GitHub at https://github.com/chopralab/lemon/tree/master/dubs.