feat(md): temperature/KE, Rg and SASA traces; fix OpenMM in deployed image

feat(md): real OpenMM production runs with accurate Ca RMSD

fix(blast): handle NCBI server overload gracefully

fix: increase axios timeout for long-running endpoints and fix Render config

feat: cross-feature auto-fill bridges — data flows between all tools via sessionStorage

fix: add optional score property to Domain type for TSV export

fix: harden BLAST pipeline against NCBI timeouts and server overload

feat: expanded Domain & Motif Analysis with all features and cross-project links

test: comprehensive validation & fuzz testing with bug fixes

fix: increase BLAST timeout from 5min to 10min for long proteins

fix: remove all rate limiters blocking pipeline runs

fix: NCBI_API_KEY not loading - blast.py read os.environ before dotenv

fix: remove NCBI rate limiting, retry only on connection errors

fix: UniProt link shows invalid URL when accession is NCBI

feat: show PDB structures, GO terms, and expanded features in UniProt panel

fix: UniProt fallback search by protein name when NCBI mapping fails

feat: Gemini fallback for AI interpretation when Groq fails

fix: Ramachandran tab hidden for proteins without PDB IDs + AI interpretation error

fix: PDB IDs like 1TIM rejected as NCBI accessions causing 400 error

fix: StructureComparison re-fetches on every render due to audit dep

fix: case-insensitive accession lookup - normalize to uppercase at entry points

fix: AlphaFold lookup for NCBI RefSeq accessions

fix: UniProt mapping resilience - skip gracefully instead of failing pipeline

perf: parallelize post-BLAST steps + fast_mode Swiss-Prot toggle

fix: BLAST reliability - API key, exponential backoff, retry, error tracking

feat: live pipeline status progression — worker pushes status to Supabase at each step

fix: add 'running' to isActive and STATUS_ORDER to prevent false 'no results' flash; show bit_score in ScoreBars

chore: increase rate limit 3/min -> 10/min for pipeline and sequencing endpoints

fix: prevent GROQ restricted-key hang in interpret and audit steps

fix: rewrite map_refseq_to_uniprot to use two-step ID mapping API

fix: correct column name 'results' -> 'result' in PATCH payload

fix: wrap sequence/length under query key for frontend AssembledContext

fix: rebind httpx.AsyncClient when event loop changes

fix: strip NCBI QBlastInfo preamble before XML parsing

fix: hydrate context_json from storage_url so frontend can render pipeline results

fix: pipeline robustness — UniProt hit fallback, sweep timeout, heartbeat

fix: BLAST pipeline crash — accession misclassification + missing error handling

fix: BLAST sequence not read - store full sequence in query_preview, fix context_json fallback

fix: BLAST pipeline stuck in queue — 3 root causes

fix: num_aromatic_rings -> n_aromatic_rings in CYP panel

feat: add smoke-test suite — ADMET/MD/function/docking endpoint validation (27 tests)

feat: ADMET 3a/3b split — mark RDKit descriptors as production, toxicity/ADMET as rule-based heuristic

fix: wrap all Fragments.fr_* calls in safe _fg() wrapper

fix: mol_volume fallback referenced labute_asa before definition

fix: MolVolume with triple fallback (CalcMolecularVolume -> Descriptors3D -> ASA estimate)

fix: MolVolume -> CalcMolecularVolume + wrap optional descriptors in try/except

fix: include smiles in docking payload dict for when ligand_smiles column is missing

fix: remove rate limiting from docking endpoint (429 error)

fix: ADMET import error + MD secondary structure accuracy

feat: industrial-grade ADMET + detailed MD/function results