Structural carryover: manuscript and public supplementary data, release 1.0

representative_sequence_pairs.csv: four parent/carry-on sequence pairs corresponding to Figures 2 and 3 (F2A, F2B, F3A, F3B). Figure 2 examples also appear in Figure S4. Experimental links are explicit; untested computational examples are not binding claims.
reference_structures/: four unmodified archived starting scaffold complexes used to define structural retention. Binder residue names may differ from the parent sequence or be UNK placeholders. Use the paired CSV for protein sequences, not PDB residue names. Do not relabel scaffold side chains as if they were a structure prediction of the parent sequence.
representative_reference_structures.csv: chain assignments, target sequences and SHA-256 checksums for those four structures. Preserve chain multiplicity when assembling target inputs; TNF-alpha has three target chains. Corresponding binder positions map in sequence order.
representative_prediction_metrics.csv: fresh-prediction metrics for the four pairs across seven predictors. These are predictions, not experimental binding measurements. Independent predictions can differ from the reported values.
experimental_binding_results.csv: all 40 submitted binder-core sequences, outcomes and tag positions. Unknown means insufficient expression in this dataset.
experimental_assay_conditions.csv: measured replicate counts and target concentration series from provider exports, plus tags and classifications.
supplementary_bli_lineage.csv: exact links for all 20 submitted optimized sequences; no sibling prediction substituted when a submission is absent from the main fresh panel.
supplementary_site_retention.csv: cohort-level residue-contact data.
supplementary_nonprotein_targets.csv: all 120 nonprotein-target outputs and metrics; internal storage locations omitted.
nonprotein_representative_metrics.csv: paired sequences and metrics for Figure S5.

The parent IDs retain correspondence with manuscript figures and tables; internal infrastructure paths and optimization runtime/configuration details are not included. All sequence values are untagged binder sequences unless explicitly identified as target sequences.

TNF-alpha assay results use the provider export downloaded on 3 October 2026. TNFA_OPT_08 is classified as no binding (two measured replicates); no apparent KD is assigned. The optimized and unoptimized TNF-alpha groups contain 6/10 and 1/10 confirmed binders, respectively.
