Description

Search for protein structural hits against a foldseek database of protein structures

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

pdb (file)

Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input)

*.{pdb,mmcif,mmjson}

meta_db (map)

Groovy Map containing sample information for the foldseek db
e.g. [ id:'test', single_end:false ]

db (directory)

foldseek database from protein structures

*

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

aln (file)

Structural comparisons file output
Query, Target, Identity, Alignment length, Mismatches, Gap openings,
Query start, Query end, Target start, Target end, E-value, Bit score

*.{m8}

versions (file)

File containing software versions

versions.yml
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Github user vagkaratzas
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Tools

foldseek
GPL v3

Foldseek: fast and accurate protein structure search

search.foldseek.com/search github.com/steineggerlab/foldseek10.1038/s41587-023-01773-0