LigandExtractor

Overview

LigandExtractor can be used to identify all ligands in a structure file from the Protein Data Bank. In addition to finding all possible ligands, it annotates any problems or particularities as so-called "skip reasons". All ligands found in the files can be specifically extracted, including their conformation, and written as an SD file. The extracted ligand files can then be used in other tools. They can be used to define a binding site for molecular docking. They are also suitable as input for conformer generation and automated design workflows.

Limitations

Currently, ligands that are covalently bound to a macromolecule cannot be written to SD files.

Software Availability

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

References

Flachsenberg, F.; Ehrt, C.; Gutermuth, T.; Rarey, M. Redocking the PDB. J Chem Inf Model 2024, 64 (1), 219-237. DOI: https://doi.org/10.1021/acs.jcim.3c01573