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.

Correspondence APIs

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)
  • http://rna.bgsu.edu/rna3dhub/rest/SeqtoUnitMapping?ife=5J7L|1|AA

Nucleotide to nucleotide alignments between RNA chains from 3D structures

This API takes as input two or more PDB chains of the same molecule and returns a pairwise or multiple alignment of the nucleotides, by presenting unit ids on the same line to indicate alignment.  Alignments are produced by Infernal alignment to the Rfam covariance model, so alignments between different species can be produced.  Our sense is that the alignments are generally good.

  • http://rna.bgsu.edu/correspondence/align_chains?chains=5J7L|1|AA,1J5E|1|A (alignment between E. coli and Thermus thermophilus small ribosomal subunits, numbering is designed to be the same, but each structure has a number of unobserved nucleotides, indicated by NULL)
  • http://rna.bgsu.edu/correspondence/align_chains?chains=5J7L|1|DA,7RQB|1|1A,7A0S|1|X,4WF9|1|X  (multiple alignment of E. coli, T. thermophilus, D. radiodurans, S. aureus large subunit ribosomal RNA)
  • http://rna.bgsu.edu/correspondence/align_chains?chains=5J7L|1|AA,1J5E|1|A,6TH6|1|Aa,4V88|1|A6,6ZMI|1|S2 (cross-domain alignment of E. coli, T. thermophilus, yeast, human by aligning all sequences to the eukaryotic SSU Rfam family; these alignments may not be as reliable as those within one domain)

Pairwise alignment diagnostic and basepair bar diagram

This API takes as input two PDB chains of the same molecule and returns a PDF which shows the alignment by listing nucleotides on the same horizontal line, a per-nucleotide score that reflects how well the alignment conserves basepairs and other pairwise interactions, and circular arcs that show the pairwise interactions in each structure.  Symmetry of the interaction arcs indicate a correct alignment.  Nested cWW basepairs are colored dark blue, long-range cWW basepairs (pseudoknots) are colored red, nested non-cWW basepairs are colored cyan, long-range non-cWW basepairs are colored green, base-phosphate interactions are colored purple, base-ribose interactions are colored orange, stacking interactions are colored yellow.  Pairwise interactions made by modified nucleotides are not shown as of 2/2/2024.  Horizontal bars are colored darker for larger per-nucleotide score.  Per-nucleotide score is larger when long-range basepairs are aligned; dark bars indicate strong evidence that the nucleotides are correctly aligned.

  • http://rna.bgsu.edu/correspondence/basepair_bar_diagram?chains=5J7L|1|AA,1J5E|1|A (E. coli and T. thermophilus SSU rRNA; very good alignment and identical numbering by design; changes in helix length around E. coli number C188 and U209 are well known but lead to small deficiencies in the alignment)
  • http://rna.bgsu.edu/correspondence/basepair_bar_diagram?chains=5J7L|1|DA,4WF9|1|X (E. coli and S. aureus LSU rRNA)
  • http://rna.bgsu.edu/correspondence/basepair_bar_diagram?chains=5J7L|1|AA,8GLP|1|S2 (E. coli and human SSU rRNA cross domain alignment; human has many insertions compared to E. coli)
  • http://rna.bgsu.edu/correspondence/basepair_bar_diagram?chains=8GLP|1|S2,4V88|1|A6 (human and yeast SSU rRNA)
  • http://rna.bgsu.edu/correspondence/basepair_bar_diagram?chains=4V9F|1|9,8GLP|1|L7 (H. marismortui and human 5S rRNA; note the scoring of the G-bulge at H.m. G78, U79)
  • http://rna.bgsu.edu/correspondence/basepair_bar_diagram?chains=4TNA|1|A,3Q1Q|1|C (tRNAs)

Annotated interactions

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

Coordinate API

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.

3D Coordinate Viewer

This API shows the 3D coordinates of selected units by constructing a URL in one of the following forms: 

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.


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:

Updated: 03/10/2024 03:17PM