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schwede
openstructure
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56c80161
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56c80161
authored
1 month ago
by
Studer Gabriel
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@@ -9,7 +9,7 @@ OpenStructure provides "actions" for general benchmarking use cases.
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/).
(compile instructions: https://openstructure.org/docs/install/).
Running the computations in containers provide a considerably easier setup than
compiling OpenStructure from source. Instructions for setup and running
equivalent computations are available for
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@@ -34,7 +34,9 @@ default output (out.json):
ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score
```
An example output can be found
[
here
](
compare-structures_example_out.json
)
An example output can be found
[
here
](
compare-structures_example_out.json
)
and
we refer to the action documentation for in-depth description of the provided
data items.
By default, model-reference chains are aligned using Needleman-Wunsch.
Many benchmarking efforts such as CASP and CAMEO assume residue numbers
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@@ -54,6 +56,8 @@ ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd
```
An example output can be found
[
here
](
compare-ligand-structures_example_out.json
)
and we refer to the action documentation for in-depth description of the provided
data items.
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
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