README.md

Structure comparison examples

OpenStructure provides "actions" for general benchmarking use cases.

• compare-structures: Focuses on comparisons involving polymer entities, i.e. protein, DNA and RNA chains
• compare-ligand-structures: Focuses on comparisons of interactions between polymer entities and non-polymer entities, i.e. small molecule ligands

The example commands here assume an OpenStructure installation (compile instructions: https://openstructure.org/docs/dev/install/). Detailed instructions for running equivalent computations are available for

• Docker: https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker
• Singularity https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity

The command

ost <ACTION> -h

will list all available options of the respective action. Both actions compute scores on an “opt-in” basis and produce output in JSON format. Example to compute global and per-residue LDDT scores, as well as as QS-scores which are written to default output (out.json):

ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score

By default, model-reference chains are aligned using Needleman-Wunsch. Many benchmarking efforts such as CASP and CAMEO assume residue numbers according to target sequence(s). Both "actions" allow to derive model-reference chain alignments according to these numbers which should be preferred in these cases. This can be enabled by adding a -rna (residue number alignment) flag:

ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score -rna

The same example also contains small molecule ligands which can be scored with:

ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd --lddt-pli

Again, it is advised to use the -rna flag if applicable. In this example, reference ligands are directly extracted from the provided mmCIF file based on "non-polymer" entity types. This only works in case of mmCIF input AND if the respective ligand is in the PDB component dictionary which defines connectivity (matching based on compound name). Container solutions come with such a dictionary which has been created at build time. Check the Docker/Singularity instructions linked above on how to set the latest dictionary, i.e. "Compound Library". You can override automatic extraction by providing SDF files with ligand coordinates and connectivity information. If the receptor is provided in PDB format, ligands must be provided in SDF format.