LifeSoaks

Overview

LifeSoaks was designed to find solvent channels in macromolecular structures solved by X-ray crystallography. It predicts their accessibility by molecules through an automated annotation of so-called bottleneck radii. It simplifies the process of manually checking a crystal structure for solvent channels. Bottleneck radii can be calculated for solvent channels and small molecule binding sites. The tool is ideally suited for channel analyses before the actual soaking experiments to select the most promising experimental conditions and crystal forms. LifeSoaks runs fully automated and will finish within seconds to minutes for moderately sized crystals.

Software Availability

We are offering LifeSoaks as part of our ProteinsPlus web service. There, users can analyze all PDB structures solved by X-ray crystallography. Please visit https://proteins.plus, upload your protein, and choose LifeSoaks.
The command-line tool LifeSoaks is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download LifeSoaks, 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 LifeSoaks. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Pletzer-Zelgert, J.; Ehrt, C.; Fender, I.; Griewel, A.; Flachsenberg, F.; Klebe, G.; Rarey, M. LifeSoaks: A Tool for Analyzing Solvent Channels in Protein Crystals and Obstacles for Soaking Experiments. Acta Crystallogr D Struct Biol 2023, 79 (Pt 9), 837-856. DOI: https://doi.org/10.1107/S205979832300582X