AltLocEnumerator

Overview

AltLocEnumerator was developed to model structural ambiguities appropriately. It handles alternate locations (AltLocs) in experimentally solved protein structures automatically. Thus, users can explore and evaluate the experimentally verified conformational space of their structure of interest. AltLocEnumerator uses a graph-based algorithm to enumerate all valid conformations that do not introduce steric clashes or chain breaks. It generates all structural variants and writes them to separate PDB files.

Software Availability

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

References

Gutermuth, T.; Sieg, J.; Stohn, T.; Rarey, M. Modeling with Alternate Locations in X-ray Protein Structures. J Chem Inf Model 2023, 63 (8), 2573-2585. DOI: https://doi.org/10.1021/acs.jcim.3c00100