Fix swapped heavy/light columns in zimmerman2020antibody_4420_kd.csv - #13
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Fix swapped heavy/light columns in zimmerman2020antibody_4420_kd.csv#13thematrixmaster wants to merge 1 commit into
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Summary
In
data/binding/zimmerman2020antibody_4420_kd.csvtheheavyandlightcolumns appear to beexchanged: the
heavycolumn holds a kappa light-chain V region and thelightcolumn holds theheavy-chain V region. This PR swaps the two columns' contents so the file matches the
heavy,lightconvention documented in the README and used by the other datasets.No sequence, measurement or row was altered — only the two columns' positions. The change was
made by exchanging the first two comma-separated fields of each line, so every other column is
preserved byte-for-byte.
Evidence
All of this is checkable from the file itself plus public references:
ANARCI chain typing, 21/21 rows.
abnumber.Chain(seq).chain_typereturnsKfor everyvalue in the
heavycolumn andHfor every value in thelightcolumn.C-terminal J motifs. Every
heavyvalue ends...TFGGGTKLEIK(a kappa J gene motif);every
lightvalue ends...WGQGTSVTVSS(a heavy J gene motif).Lengths match PDB 1FLR the other way round. The
heavycolumn is 112 aa and thelightcolumn 118 aa. In 1FLR (the 4-4-20 Fab) the light chain variable domain is 112 aa and the
heavy 118 aa.
Cross-check against the other 4-4-20 dataset in FLAb. The
heavycolumn of this file isbyte-identical to the
lightcolumn ofdata/expression/adams2017measuring_4420-fluorescein_exp_er.csv, which labels that samesequence as the light chain.
How it was found
While converting FLAb for an antibody variant-effect benchmark, we searched GenBank for published
nucleotide sequences matching each dataset's wildtype by exact six-frame translation. The 4-4-20
light-chain cDNA record matched this file's
heavycolumn, which surfaced the swap. A chain-typecheck with ANARCI then confirmed it, and across FLAb's other 164 datasets this is the only file
affected.
Reproducing
Thanks for assembling and maintaining FLAb — it has been very useful to us.