@platforma-open/milaboratories.antibody-sequence-liabilities 5.2.0 → 5.2.1

package/block-pack/CHANGELOG.md

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+## 1.0.0
+
+Initial release.

package/block-pack/description.md

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+# Overview
+
+Identifies sequence liabilities in antibody/TCR or peptide amino acid sequences and classifies them by fixability — how tractable each liability is to engineer away. This lets you distinguish candidates that need a quick conservative substitution from those requiring significant reengineering or that are not viable.
+
+The block evaluates sequences for deamidation (`N[GS]`, `N[AHNT]`, `[STK]N`), fragmentation (`DP`, `TS`), isomerization (`D[DGHST]`), N-linked glycosylation (`N[^P][ST]`), oxidation-prone residues (tryptophan, methionine), cysteine issues (missing or extra), and integrin binding motifs. The set of applicable rules adapts to modality: antibody/TCR inputs are evaluated per CDR and framework region and include architecture-specific cysteine and hinge-fragmentation checks, while peptide and amplicon variant inputs apply a flat backbone-chemistry rule set to the whole sequence, without region or cysteine-architecture checks.
+
+Two output columns are emitted for both modalities:
+
+- **Developability risk** — `None` / `Low` / `Medium` / `High` / `Very High` / `Non-Developable`: engineering severity for fixable liabilities at the lower end of the scale; `Very High` when a Hard to fix liability is present (e.g. Extra Cysteines); `Non-Developable` when a Structural liability is present (e.g. Missing Cysteines)
+- **Developability cost** — continuous score: sum of engineering effort weighted by fixability class (antibody mode also weights by region importance); lower = easier to engineer
+
+Antibody/TCR inputs additionally produce:
+- **Is Productive** — `Pass`/`Fail`: fails on stop codons or out-of-frame sequences
+
+For antibody/TCR inputs you can restrict the scan to specific regions. Use this when the parental
+scaffold carries liabilities you already accept and only the engineered region should be scored.
+`Is Productive` still covers the whole molecule.
+
+You can extend the predefined liability set with custom motifs defined in the block settings or imported from a JSON file.

package/block-pack/manifest.json

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