Changelog

All notable changes to this project. Each entry links to its full per-version file in changelog/.

0.9.0 — 2026-11-03 · ⚠️ Breaking · 🛡️ Security

Source organisms are now lists, Foldseek hits and sequence hits carry alignments, and best_available, isoforms, merged accessions, InterPro paging, and coordinate windows are corrected. Ships the protein-guide skill; three call shapes are newly rejected.

0.8.7 — 2026-10-16

Reach the full annotation set with independent class paging and source-preserved variant and domain records.

0.8.6 — 2026-10-07

Framework ^0.13.6 → ^0.13.13: tool errors carry a request ID, declared recovery hints are filled in by the framework, and error data no longer carries stacks or request context; Docker builds install in a build-platform deps stage, and the registry's npm entries launch through npx with the HTTP entry pinned to HTTP.

0.8.5 — 2026-09-22

protein_track_ligands find_ligand reports candidate-pool totals, binding_site adds author residue numbering and pages ligand instances.

0.8.4 — 2026-09-22

Fixes protein_find_similar by:structure exposing only Foldseek's first chain query and ranking hits per-database instead of by combined score.

0.8.3 — 2026-09-22

Fixes computed-model sequence-hit IDs, dead coordinate-file URLs, reversed alignment-resume labeling, and false zero-match notices past the last results page; tool descriptions reworded to drop implementation leaks.

0.8.2 — 2026-09-21

Adopts mcp-ts-core 0.13.6: argument rejections carry recovery hints (0.13.3), tool arguments pass pre-validation aliasing (0.13.4), and tool-error text names its reason (0.13.5); server instructions rewritten for workflow chaining.

0.8.1 — 2026-09-16

Adopts @cyanheads/mcp-ts-core 0.13.2, declaring stateless HTTP session mode in source, plus dependency and skills-tree maintenance.

0.8.0 — 2026-09-09 · ⚠️ Breaking

protein_find_similar rejects fields the selected by mode can't consume and paginates completed structure searches with a re-usable ticket; protein_get_annotations reclassifies a missing or malformed identifier as InvalidParams; plus RCSB GraphQL, ligand-formula, and get_structure text-surface fixes.

0.7.0 — 2026-09-08 · ⚠️ Breaking

protein_get_structure exposes per-entity authAsymIds/labelAsymIds chain namespaces plus entry detail (ligands, molecular weight, release date), accumulates every advisory instead of overwriting, and gates the coordinate overflow budget on a single oversized file too; pdb://{entry_id}'s polymerEntities[].chains is renamed to authAsymIds.

0.6.0 — 2026-09-08 · ⚠️ Breaking

protein_analyze_collection's truncation notice covers nested cross-tab children and empty scopes, interval routes to whichever group_by dimension can consume it and is narrowed to RCSB's supported values, and protein_search_structures rejects sequence-only thresholds and surfaces capped-facet recovery guidance.

0.5.3 — 2026-08-30

RCSB-backed tools support offset pagination; structure searches accept method or resolution criteria alone, retain chainable sequence-hit IDs, and enrich every entry on a returned sequence page.

0.5.2 — 2026-08-25 · ⚠️ Breaking

Tool inputs are strict now — an unrecognized argument key is rejected instead of stripped — and cache hints let 2026-07-28 clients hold listings and resource reads for up to an hour; HTTP session mode is pinned to stateless.

0.5.1 — 2026-08-16

protein_analyze_collection reports the realized bucket total, and bucket_limit's per-dimension-level semantics are now stated explicitly everywhere it's described.

0.5.0 — 2026-08-16 · ⚠️ Breaking

protein_analyze_collection's nested facet child is now a single optional field instead of an array, and all three collection/comparison tools reject duplicate or ambiguous inputs with typed errors.

0.4.2 — 2026-08-16

protein_find_similar's Foldseek identity score now returns a 0–1 fraction as declared, protein_get_structure and af:// no longer lose a whole predicted-source batch to one malformed ID, and protein_compare_structures reports per-structure modeled-residue count and coverage.

0.4.1 — 2026-08-16

protein_search_structures' default content_type union now returns computed models, facet dimensions disclose coverage gaps and empty-dimension explanations, and protein_get_structure credits computed-model IDs to their modelling provider instead of the PDB.

0.4.0 — 2026-07-03

protein_get_annotations gains a per-class limit to cap features/variants/domains independently, and protein_compare_structures documents TM-score's length-normalization sensitivity to terminal length differences.

0.3.3 — 2026-07-03

protein_analyze_collection accepts stringified numeric inputs, protein_track_ligands find_ligand decouples its ranking pool from the display limit, and numeric facet histogram buckets carry explicit rangeFrom/rangeTo bounds.

0.3.2 — 2026-07-03

protein_track_ligands find_ligand now ranks by deposition frequency instead of name order; structures_with_ligand sorts by resolution instead of a constant score; protein_find_similar sequence hits emit a chainable entry id with the entity id preserved separately.

0.3.1 — 2026-07-03

best_available confidence scores are now scale-correct and self-describing instead of overloading meanPlddt; experimental best_available picks return the full cif/pdb/bcif coordinate set, matching source: experimental.

0.3.0 — 2026-07-03

protein_get_annotations disambiguates multi-chain PDB entries via a new chain input; protein_get_structure and protein_get_annotations both carry upstream data-source attribution (license + citation).

0.2.1 — 2026-07-03

Nested cross-tab facet children now carry a truncated flag; declared error recovery hints reach the wire; protein_track_ligands binding_site honors limit.

0.2.0 — 2026-07-03 · 🛡️ Security

Resume protein_find_similar and protein_compare_structures jobs by ticket/UUID instead of resubmitting; compare_structures structures cap widened to the configured 2–25 range with a truncation notice; dependency refresh clears a moderate js-yaml advisory.

0.1.4 — 2026-06-23

Narrow the public description and server instructions from 'structure & function' to 'structure & annotation'. No behavior changes.

0.1.3 — 2026-06-20

Maintenance: mcp-ts-core ^0.10.6 → ^0.10.9, re-synced framework scripts/skills and devcheck guards. No behavior changes.

0.1.2 — 2026-06-18

Published metadata now advertises the public hosted Streamable HTTP endpoint at https://protein.caseyjhand.com/mcp.

0.1.1 — 2026-06-18

Zero-result RCSB searches return empty sets sub-second instead of a retried outage error; protein_track_ligands missing-param guards now classify as InvalidParams; protein_get_structure best_available surfaces the chosen pdbId.

0.1.0 — 2026-06-15

Initial release: federated protein structure & function across PDB, AlphaFold, UniProt, InterPro, and Foldseek — 7 tools, 2 resources.