WarPP

Overview

WarPP predicts the position and orientation of water molecules in small-molecule binding sites. It places and scores water molecules in binding sites of crystallographic structures based on EDIAscorer results and interaction geometries as known from experimentally solved protein structures. WarPP was validated on a high-quality set of 1,500 protein-ligand complexes, containing 20,000 crystallographically observed water molecules. It is sufficiently fast for high-throughput analyses. It correctly places water molecules in approx. 80% of the cases. Users can export the predictions as PDB files for, e.g., molecular docking with JAMDA.

Software Availability

We are offering WarPP as part of our ProteinsPlus web service for protein structures with bound ligands. Please visit https://proteins.plus, upload your protein, and choose WarPP.

WarPP is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download WarPP, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run WarPP. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Nittinger, E.; Flachsenberg, F.; Bietz, S.; Lange, G.; Klein, R.; Rarey, M. Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. J Chem Inf Model 2018, 58 (8), 1625-1637. DOI: https://doi.org/10.1021/acs.jcim.8b00271