Folding without glutamine: proteome-scale removal of a canonical amino acid Dataset

This record contains the data and analysis code underlying the figures of the study Folding without glutamine: proteome-scale removal of a canonical amino acid. Using the Escherichia coli reference proteome as a test case, the work asks whether an entire canonical amino acid can be removed from every protein in a proteome without large structural consequences. It combines ProteinMPNN- and MSA-derived "keep-scores" that rank the twenty amino acids by replaceability, structural comparisons (AlphaFold2/3, ESMFold, FoldMason, flexible alignment, BioEmu, and PyRosetta) of glutamine-free and per-amino-acid-recoded proteomes against their AlphaFoldDB references, and experimental validation of a glutamine-free TEM-1 β-lactamase. The deposit is five files: manifest.md and scripts.md (documentation), and three archives — bin.tgz (scripts), data.tgz (data), and a3m.tgz (the AlphaFold input alignments); manifest.md describes every item and maps it to the figure it supports. The deposit holds the data underlying the figures and the research code as it was used, with standard third-party tool steps documented in the paper's Methods with their versions.