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/andmanifest.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.