| --- |
| pretty_name: AFDB v6 structure shards and derived data |
| tags: |
| - protein-structure |
| - alphafold |
| --- |
| |
| # AFDB v6 structure shards and derived data |
|
|
| This repository hosts structural data, annotation tables and saved analysis |
| outputs used by the GPBridge project. A directory's publication does not imply |
| that it is a final training release; consult its data manifests and provenance. |
|
|
| Project code, internal reports, experiment material and collaborator handovers |
| are maintained in the access-controlled repository: |
| https://github.com/ZhanghanNi/GPBridge |
|
|
| Authorized collaborators should obtain the workflow and instructions there. |
| Hugging Face is the data store, not the current source of project code. |
|
|
| ## Data layout |
|
|
| - `shards/` and `manifest.jsonl`: AFDB v6 Foldcomp structure shards and inventory. |
| - `annotations/`: saved annotation outputs and mapping tables. |
| - `results/`, `recovery/`, `enzymm/`: saved retrieval results and derived tables. |
| - `alphafill/`, `ligands/`: coordinate contexts and source provenance. |
|
|
| The original Foldcomp collection comprises 241,070,489 records in 483 shards. |
| This is the source collection's coverage, not the nominal size of all AFDB. |
| Derived collections have their own scopes and manifests. |
|
|
| ## Sources and attribution |
|
|
| - AlphaFold DB: https://alphafold.ebi.ac.uk/ (CC BY 4.0). Cite the original |
| AlphaFold and AlphaFold DB publications required by that resource. |
| - Foldcomp: https://github.com/steineggerlab/foldcomp. The structure shards |
| repackage `afdb_uniprot_v6`; they are not new predictions. |
| - M-CSA: https://www.ebi.ac.uk/thornton-srv/m-csa/. Cite Ribeiro et al., |
| Nucleic Acids Research (2018), DOI 10.1093/nar/gkx1012. |
| - Experimental coordinate sources: Protein Data Bank, https://www.wwpdb.org/. |
| - AlphaFill: https://alphafill.eu/. Retain source and transplant provenance. |
| - EnzyMM: https://github.com/RayHackett/enzymm. |
| - Folddisco: https://github.com/steineggerlab/folddisco. |
|
|
| Upstream terms apply separately to their respective assets. No single new |
| license is asserted over this mixed-source collection. |
|
|
