StructureProfiler

Overview

Three-dimensional protein structures play a vital role in drug design. Thorough examination of the available data before usage in experimentation and method validation is highly recommended. StructureProfiler assists in automatically profiling structures ranging from model characteristics like low R factor over active site features such as bond lengths in expected ranges to ligand properties such as electron density coverage and frequently seen torsion angles.

Method

The criteria catalogue implemented in Structureprofiler is based on the Astex Diverse Set, the Iridium HT, and the Platinum set of criterias. It is supplied with B factor checks, the search for uncommon torsion angles, an inhouse intra- and intermolecular clash criterion and the recently published EDIAm 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 forth combined catalogue.

StructureProfiler Data Set

On a regular schedule, the PDB is scanned by the tool with the four configurations to assemble an up to date list of ligands in active sites in structures passing all tests of the respective configuration. More information can be found on the StructureProfiler Data Set Homepage.

Software Availability

The command-line tool StructureProfiler is freely available for academic users for Linux(64 and 32bit) as well as Mac and Windows as part of our NAOMI ChemBio Suite. Non-academic users can get an evaluation license free of charge. No setup steps are required to run StructureProfiler. All feedback is highly appreciated.

People and References

Meyder, A.; Kampen, S.; Sieg, J.; Fährrolfes, R.; Friedrich, N.-O.; Flachsenberg, F.; Rarey, M. (2018) StructureProfiler: An all-in-one Tool for 3D Protein Structure Profiling . Bioinformatics