Annotating PDB Files with FR3D
FR3D software can be used not only for searching RNA 3D structures, but also for annotating pairwise interactions found in these structures. Currently FR3D analyzes:
- basepair interactions according to the Leontis-Westhof nomenclature
- base-stacking interactions
- base-phosphate interactions as described by Zirbel et al.
- base-ribose interactions (these annotations are in beta right now).
FR3D can annotate interactions in PDB files produced by 3D structure prediction software, such as FARFAR or RNA 1-2-3. Crystallographers may also be interested in analyzing FR3D annotations prior to submitting their 3D structures to PDB. Alternative programs for annotating pairwise interactions include RNAView and MC-Annotate.
To annotate PDB files with FR3D:
- download FR3D from the official FR3D repository and follow the instructions in Readme.
- download and run this sample code for outputting pairwise interactions in csv format. The sample code is published as a Github gist, so please feel free to edit and discuss it.
Note that it’s not necessary to run FR3D on 3D structures already available at PDB because all RNA 3D structures are automatically annotated by RNA 3D Hub every week. FR3D annotations are made available in the RNA Structure Atlas, where pairwise interactions can be viewed and downloaded using the web interface (example: basepair interactions in 1S72) or by using our new API.