| name | foldcomp |
| description | Foldcomp — compress and index large protein structure sets (Steinegger lab) for efficient storage and random access before Foldseek-scale searches. Use when: (1) Archiving AFDB-scale PDB collections, (2) Reducing disk for structure search pipelines, (3) Extracting sequences/pLDDT from Foldcomp DBs. Upstream: https://github.com/steineggerlab/foldcomp. Route via homology-search with foldseek.
|
| license | MIT |
| category | analysis-tools |
| tags | ["Foldcomp","structure","compression","AFDB","Foldseek"] |
| upstream | https://github.com/steineggerlab/foldcomp |
| stage | function |
Foldcomp
Upstream: steineggerlab/foldcomp
Citation
Kim, H., Mirdita, M. & Steinegger, M. Foldcomp: a library and format for
compressing and indexing large protein structure sets. Bioinformatics 39,
btad153 (2023). https://doi.org/10.1093/bioinformatics/btad153
See also docs/references.md.
Analytical thinking
Structure search needs structures on disk. Foldcomp provides a compact
format + index for large PDB/mmCIF collections used with Foldseek-family
tools. Infrastructure skill — not a homology algorithm itself.
How to run
foldcomp compress input_structures/ structures.fcz
foldcomp decompress structures.fcz out_dir/
Decision tree
Many protein structures to store/search?
├─ Compress/index archive → foldcomp
├─ Search → foldseek / folddisco / foldmason
└─ Sequence-only path → foldseek + ProstT5
Related skills
foldseek · foldmason · folddisco · homology-search · tool-selection
