Building 3D RNA Databases

The (prepare_data) contains all the necessary code to build databases of annotated RNA 3D structures, and the user interfaces with it through the rnaglib_prepare_data command line script. Database creation follows the following steps:

  • Fetching the raw RNA structures from either:

  • For each structure, run fr3d-python.

  • Store fr3d-python output in a networkx Graph object

  • Include addidtional annotations to the graph (e.g. small molecule binding info, chemical modifications, etc.)

Quickstart

Print the help message:

$ rnaglib_prepare_data -h

To run a quick debug build with default values:

$ rnaglib_prepare_data -s structures/ --tag first_build -o builds/ -d

Data versioning

The optional argument –tag is used to name the folder containing the final output. For our distributions we use rnaglib-<’all’ or ‘nr’><’-annotated’ or ‘’><’-chopped’ or ‘’>-<version> depending on the build options. We distribute data builds with all available RNAs and assign all to the tag, and non-redundant structures according to the [BGSU Representative Set](https://www.bgsu.edu/research/rna/databases/non-redundant-list.html).

Output

After running the –debug test run above, your ./builds/ folder will contain a single sub-folder called ./builds/graphs with 10 .json files and a file ./builds/graphs/errors.csv. Each of these JSONs contains the annotated RNAs and the CSV contains a list of RNAs that failed to build and the failure reason.

Data building options

  • –nr only outputs RNAs from the non-redundant set from BGSU

Hosting