StructureProfiler

Overview

Three-dimensional protein structures play a vital role in drug design. Structure-based design necessitates an in-depth examination of the available quality data before using the structure in computational experiments and for method evaluation. StructureProfiler assists in automatically profiling sets of protein-ligand complex structures based on multiple quality indicators, ranging from model characteristics, e.g., the R factor, and active site features, e.g., bond length deviations, to ligand properties such as electron density support and the validity of torsion angles.

Method

The quality measures implemented in StructureProfiler are based on the Astex Diverse Set, the Iridium HT, and the Platinum set of criteria. It offers B-factor checks, the detection of uncommon torsion angles, an intra- and intermolecular clash detection, and EDIAscorer results to scan for conspicuous electron density support. The tool is highly configurable and thus supplied with four configuration sets, three related to the aforementioned data sets and a fourth combined catalogue.

Note that the various scores to measure electron density support of the model are replaced by EDIA values calculated with EDIAscorer in all configurations.

Datasets

A dataset fulfilling all tests of the “Combined” StructureProfiler configuration can be found at https://www.zbh.uni-hamburg.de/forschung/amd/datasets/structureprofiler-dataset.html.

Software Availability

We are offering StructureProfiler as part of our ProteinsPlus web service for single PDB structures. Please visit https://proteins.plus, upload your protein, and choose StructureProfiler.

The command-line tool StructureProfiler is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download StructureProfiler, 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 StructureProfiler. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Meyder, A.; Kampen, S.; Sieg, J.; Fährrolfes, R.; Friedrich, N. O.; Flachsenberg, F.; Rarey, M. StructureProfiler: An All-In-One Tool for 3D Protein Structure Profiling. Bioinformatics 2019, 35 (5), 874-876. DOI: https://doi.org/10.1093/bioinformatics/bty692