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).
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.
- Using unit IDs to get coordinates: http://rna.bgsu.edu/rna3dhub/rest/getCoordinates?coord=2QBG|1|A|G|69,2QBG|1|A|G|107
- Using loop ID to get coordinates: http://rna.bgsu.edu/rna3dhub/rest/getCoordinates?coord=IL_1S72_009
3D Coordinate Viewer
This API shows the 3D coordinates of selected units by constructing a URL of the following form:
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.
Sequence position to unit ID mapping
This API takes as input a PDB ID, model, and 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. Only works for RNA.
Unit ID to unit ID mapping within 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/corr-server/pairwise_structure?ife1=5J7L|1|AA&ife2=5J7L|1|BA (E. coli 16S)
- http://rna.bgsu.edu/corr-server/pairwise_structure?ife1=4V88|1|A6&ife2=5TBW|1|sR (Yeast 18S)
- http://rna.bgsu.edu/corr-server/pairwise_structure?ife1=3A3A|1|A&ife2=4ZDP|1|E (Human selenocysteine tRNA)
- http://rna.bgsu.edu/corr-server/pairwise_structure?ife1=4V9F|1|0&ife2=1S72|1|0 (H. marismortui LSU, where 1S72|1|0 has unobserved nucleotides from 971 to 998)
RSR / RSRZ API
This API 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:
- Using unit ids to get RSR: http://rna.bgsu.edu/rna3dhub/rest/getRSR?quality=1FJG|1|A|A|16,1FJG|1|A|C|18
- Using unit ids to get RSRZ: http://rna.bgsu.edu/rna3dhub/rest/getRSRZ?quality=1FJG|1|A|A|16,1FJG|1|A|C|18
- Using a loop id to get RSR: http://rna.bgsu.edu/rna3dhub/rest/getRSR?quality=HL_1FJG_001
- Using a loop id to get RSRZ: http://rna.bgsu.edu/rna3dhub/rest/getRSRZ?quality=HL_1FJG_001