Several APIs are available, where one can input unit ids or loop ids or chain ids and get back useful information. Note that our site uses author-assigned chain identifiers (auth_asym_id). Read about unit ids that we use to uniquely specify each nucleotide or amino acid in each 3D structure.
Many of the URLs below need to be copied and pasted; they aren't active links because this university page won't allow active links.
Unit ID to unit ID mapping between two chains in an RNA equivalence class
This API takes as input two RNA chain IDs and returns a listing of the corresponding unit IDs, as determined by the alignment of the experimental sequences for the chains. Note that only complete rows are listed; when a nucleotide is not resolved or does not exist in one structure, neither unit ID is listed.
- http://rna.bgsu.edu/correspondence/pairwise_structure?chain1=5J7L|1|AA&chain2=5J7L|1|BA (E. coli 16S)
- http://rna.bgsu.edu/correspondence/pairwise_structure?chain1=4V88|1|A6&chain2=5TBW|1|sR (Yeast 18S)
- http://rna.bgsu.edu/correspondence/pairwise_structure?chain1=3A3A|1|A&chain2=4ZDP|1|E (Human selenocysteine tRNA)
- http://rna.bgsu.edu/correspondence/pairwise_structure?chain1=4V9F|1|0&chain2=1S72|1|0 (H. marismortui LSU, where 1S72|1|0 has unobserved nucleotides from 971 to 998)
Corresponding nucleotides and pairwise interactions across an equivalence class
This API takes as input one or more unit ids from an RNA 3D structure and returns unit ids of corresponding nucleotides across the equivalence class, along with FR3D-annotated pairwise interactions between them. The header line indicates the order in which the nucleotides and the basepairs are listed.
- http://rna.bgsu.edu/correspondence/pairwise_interactions?resolution_threshold=4.0&exp_method=xray&selection_type=unit_id&selection=5J7L|1|AA|C|186 Individual nucleotide, x-ray experimental method
- http://rna.bgsu.edu/correspondence/pairwise_interactions?resolution_threshold=4.0&exp_method=em&selection_type=unit_id&selection=5J7L|1|AA|C|186,5J7L|1|AA|G|191 Basepair, cryo-em experimental method
- http://rna.bgsu.edu/correspondence/pairwise_interactions?resolution_threshold=3.0&exp_method=all&selection_type=unit_id&selection=6ZMI|1|S2|A|11,6ZMI|1|S2|A|1200,6ZMI|1|S2|A|1357 Base triple, all experimental methods, lower resolution cutoff
- http://rna.bgsu.edu/correspondence/pairwise_interactions?resolution_threshold=3.0&exp_method=all&chain=6ZMI|1|S2&selection_type=res_num&selection=11,1200,1357 Base triple using short format
- http://rna.bgsu.edu/correspondence/pairwise_interactions?resolution_threshold=all&exp_method=all&selection_type=loop_id&selection=HL_5J7L_001 Hairpin loop, all resolutions, all methods
Sequence position to unit ID mapping
This API takes as input a PDB ID, model, and RNA chain and gives as output a listing of all experimental sequence positions and the corresponding unit ID, if the coordinates of the unit were observed in the PDB file.
- http://rna.bgsu.edu/rna3dhub/rest/SeqtoUnitMapping?ife=1S72|1|0 (shows unobserved nucleotides and different numbering)
Pairwise interactions for given nucleotides or loop
This API takes as input a loop or individual nucleotides and returns a list of nucleotides and the pairwise interactions they make.
- http://rna.bgsu.edu/correspondence/pairwise_interactions_single?selection_type=loop_id&selection=HL_5J7L_001 Hairpin loop
- http://rna.bgsu.edu/correspondence/pairwise_interactions_single?selection_type=unit_id&selection=5J7L|1|AA|A|320,5J7L|1|AA|A|321,5J7L|1|AA|C|322 Unit IDs
- http://rna.bgsu.edu/correspondence/pairwise_interactions_single?chain=5J7L|1|AA&selection_type=res_num&selection=320,321,322 Shorthand notation using residue numbers
Coordinate and data quality APIs
Coordinates is a web service to retrieve the coordinates of a unit given the unit ID, or a loop given the loop id. What is returned is in mmCIF format, with the selected units in Model 1 and units within 16 Angstroms in Model 2.
- http://rna.bgsu.edu/rna3dhub/rest/getCoordinates?coord=2QBG|1|A|G|69,2QBG|1|A|G|107 Using unit IDs to get coordinates
- http://rna.bgsu.edu/rna3dhub/rest/getCoordinates?coord=IL_1S72_009 Using loop ID to get coordinates
3D Coordinate Viewer
This API shows the 3D coordinates of selected units by constructing a URL in one of the following form:
- http://rna.bgsu.edu/rna3dhub/display3D/unitid/1S72|1|0|A|965,1S72|1|0|U|1003,1S72|1|H|HIS|92 (unit ids including amino acids)
- http://rna.bgsu.edu/rna3dhub/display3D/chain/1QTQ|1|B (entire chain)
- http://rna.bgsu.edu/rna3dhub/display3D/chain/5J7L|1|AA (entire chain)
In the first link, note that individual units are listed, separated by commas. This example shows a UA cWW basepair interacting with an amino acid. One can provide such links to easily direct readers of a website or article to a view of the coordinates.
RSR / RSRZ API
This API takes as input unit ids or loop ids and returns RSR and RSRZ values for specified units or loops, in JSON format. This allows programmatic access to these structure quality data for individual units or sets of units. Construct a request using the following forms:
- http://rna.bgsu.edu/rna3dhub/rest/getRSR?quality=1FJG|1|A|A|16,1FJG|1|A|C|18 Using unit ids to get RSR
- http://rna.bgsu.edu/rna3dhub/rest/getRSRZ?quality=1FJG|1|A|A|16,1FJG|1|A|C|18 Use unit ids to get RSRZ
- http://rna.bgsu.edu/rna3dhub/rest/getRSR?quality=HL_1FJG_001 Use a loop id to get RSR
- http://rna.bgsu.edu/rna3dhub/rest/getRSRZ?quality=HL_1FJG_001 Using a loop id to get RSRZ
Updated: 05/14/2022 09:20AM