| --- |
| license: cc0-1.0 |
| task_categories: |
| - text-generation |
| - fill-mask |
| - other |
| tags: |
| - RNA |
| - RNAcentral |
| - PDB |
| - mmCIF |
| - structural-biology |
| - inverse-folding |
| pretty_name: RNAcentral-Struct |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # RNAcentral-Struct |
|
|
| RNAcentral-Struct is a structure subset derived from the official RNAcentral PDB cross-reference table. It contains every unique PDB entry referenced by RNAcentral `current_release/id_mapping/database_mappings/pdb.tsv`, downloaded as mmCIF from official PDB mirrors. |
|
|
| This dataset is intended for RNA structure-conditioned modeling, inverse folding, and cross-reference analysis. RNAcentral itself is a sequence and annotation resource; the 3D coordinates here come from wwPDB/RCSB/PDBe entries linked by RNAcentral. |
|
|
| ## Contents |
|
|
| - `structures/*.cif`: 7,279 unique mmCIF files, one per four-character PDB entry ID. |
| - `metadata/rnacentral_pdb.tsv`: the RNAcentral official PDB cross-reference table used to build this package. |
| - `metadata/pdb_structure_mapping_all.csv`: all RNAcentral chain-level mappings to the downloaded mmCIF files. |
| - `metadata/pdb_structure_mapping_downloaded.csv`: mappings whose referenced mmCIF file is present. For this release it matches the full mapping table. |
| - `metadata/manifest.json`: machine-readable summary. |
| - `metadata/summary.tsv`: compact summary. |
| - `metadata/cif_sizes.tsv`: byte size for each downloaded mmCIF file. |
| - `metadata/download_failures.json`: download failure list. This release has no failures. |
| - `scripts/rnacentral_all_cif_downloader.py`: downloader used to reproduce the package. |
|
|
| ## Summary |
|
|
| | field | value | |
| |---|---:| |
| | RNAcentral PDB mapping rows | 18,967 | |
| | Unique RNAcentral UPI IDs | 4,750 | |
| | Unique PDB/mmCIF entries | 7,279 | |
| | Downloaded mmCIF files | 7,279 | |
| | Download failures | 0 | |
| | Uncompressed package size | ~54 GB | |
|
|
| ## Mapping Semantics |
|
|
| RNAcentral `pdb.tsv` maps RNAcentral UPI IDs to PDB chain-level accessions such as `4UG0_L8`. The four-character prefix, `4UG0`, is the PDB entry ID and corresponds to one mmCIF file: `structures/4ug0.cif`. The suffix identifies a chain or chain-like accession within that entry. Multiple RNAcentral rows can therefore reference the same mmCIF file. |
|
|
| ## Reproducibility |
|
|
| The source mapping file is: |
|
|
| ```text |
| https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv |
| ``` |
|
|
| The downloader extracts unique PDB IDs from that mapping and downloads `{PDB_ID}.cif` from RCSB with PDBe fallback. |
|
|
| ## License |
|
|
| RNAcentral sequence metadata is distributed under CC0. PDB coordinate files are redistributed according to wwPDB/RCSB/PDBe terms. Please cite RNAcentral and wwPDB/PDB resources when using this dataset. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{rnacentral2021, |
| author = {{RNAcentral Consortium}}, |
| title = {{RNAcentral} 2021: secondary structure integration, improved sequence search and new member databases}, |
| journal = {Nucleic Acids Research}, |
| volume = {49}, |
| number = {D1}, |
| pages = {D212--D220}, |
| year = {2021}, |
| doi = {10.1093/nar/gkaa921} |
| } |
| ``` |
|
|
