FR3D stands for "Find RNA 3D" and is commonly pronounced "Fred". FR3D enables searching and annotating RNA 3D structures and supports the mmCIF format.

Originally written in Matlab, this repository is a re-implementation of FR3D in Python. FR3D and FR3D Python are developed by the BGSU RNA Bioinformatics group.

Get started with FR3D using containers with Docker, Podman, or Singularity.

1. Get a Docker image

   docker pull ghcr.io/bgsu-rna/fr3d-python
   # tag the image with a shorter name for convenience
   docker tag ghcr.io/bgsu-rna/fr3d-python fr3d-python
   

   Alternatively, clone the repo and build locally:

   git clone https://github.com/BGSU-RNA/fr3d-python
   docker build -t fr3d-python .
   

   Notes for M1 Mac users

   To build a Docker image on M1 Macs use docker buildx to specify the target platform in order to be able to install all the dependencies:

   docker buildx install
   docker buildx build -t fr3d-python --platform linux/amd64 .

2. Annotate RNA 3D structures with basepair interactions

   docker run -v <path_to_input>:/rna/input -v <path_to_output>:/rna/output fr3d-python python fr3d/classifiers/NA_pairwise_interactions.py -i /rna/input -o /rna/output <pdb_id>
   

   where

   • path_to_input is the folder where cif files are stored (if a file does not exist already it will downloaded)
   • path_to_output is the folder where the results will be generated
   • pdb_id is the PDB identifier of the structure to be annotated (for example, 1S72). Multiple PDB identifiers can be specified
   • Optional flag determines which output files are generated
     • -c basepair outputs a file listing basepairs in the 12 Leontis-Westhof families
     • -c basepair_detail outputs Leontis-Westhof pairs with more detail about asymmetric pairs and with bifurcated and alternative pairs
     • -c sO outputs a file with base-oxygen stacking annotations
     • -c basepair,cO outputs both basepair and sO annotation files; don't put spaces between the category types

Note that as of April 2022, NA_pairwise_interactions.py outputs annotations of RNA basepairs, including basepairs made by some modified nucleotides, but this is in a test phase, and not all basepairs are being annotated. Work to refine the basepair annotations will continue in Spring 2023; nearly done!

The program NA_pairwise_interactions.py generates tab-separated files called <pdb_id>_basepairs.txt that list basepair interactions between pairs of nucleotides (an RNA 3D structure can contain 0 or more basepairs). The files contain the following fields:

• Unit ID of the first nucleotide in the Unit ID format
• basepair interaction between the first and second nucleotides, defined according to the Leontis-Westhof nomenclature
• Unit ID of the second nucleotide
• number of interactions crossed by the basepair (0 for nested basepairs or an integer for non-nested basepairs)

For example:

1S72|1|0|A|1193	tSH	1S72|1|0|U|1205	0
1S72|1|0|A|631	tSH	1S72|1|0|U|2607	25

git clone https://github.com/BGSU-RNA/fr3d-python
cd fr3d-python
python -m pip install .

⚠️ Any time files such as fr3d/cif/reader.py get edited, you need to rerun the python -m pip install . command.

fr3d-python requires PDBx. Follow instructions at wwPDB to install PDBx on your local machine and place in your Python path.

In order to use FR3D in Python 3, you will need to install the mmcif-pdbx package:

pip install mmcif-pdbx

This will put the PDBx package in your Python path.

Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux
fsutil.exe file setCaseSensitiveInfo <path to folder> enable

Navigate to the classifiers folder and run the following command to ensure that the installation was successful:

python NA_pairwise_interactions.py --help

You can update localpath.py to represent your file structure. Alternatively, use the --input (-i) and --output (-o) flags to specify the location of your input cif files and the output text files.

For example, if you already have the .cif file downloaded, use the --input flag to specify the directory your cif file is in:

python NA_pairwise_interactions.py --input <path_to_input> <pdb_id>

Additionally, if you don't have the cif file in your localpath, you can run

python NA_pairwise_interactions.py <pdb_id>.cif

and this will download the file for processing and run the program.

Output can be specified using the -o or --output tags, for example:

python NA_pairwise_interactions.py --output <path_to_output> <pdb_id>

This will write where you wish to output your annotations. If the specified directory doesn't exist, one will be made.

If you have any questions or feature requests, feel free to submit an issue or get in touch via a contact form on the website of the BGSU RNA Bioinformatics group.