feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

feat: optimize CASTp SASA with KDTree, add sequence input to CASTp + Structure Prep, ESMFold integration for unknown genes

feat: structure preparation pipeline — broken chains → SWISS-MODEL repair → PyMOL cleanup → fpocket + CASTp

feat: add CASTp pockets, SWISS-MODEL, ESMFold + fix Dockerfiles

chore: remove NGS rate limits

feat: add igv.js genome browser + proper 6-step NGS pipeline

fix: NGS pipeline stuck in queued - worker fallback + migration fix

feat: add full 6-step NGS pipeline + fix sequencing WinError 193

feat(pipeline): multi-database UniProt identifier resolution

fix(pipeline): stop abandoning slow NCBI BLAST jobs + EBI fallback

feat(admet): ProTox 3.0 ML toxicity prediction — backend client + endpoint, frontend ProTox tab, restored sidebar chevron

feat(seq-tools): motif categories & structure overlay, dot-plot scoring & features, cross-tool links

feat(seq-tools): add sequence utilities, motif scanner and dot plot tools with frontend pages

feat(primers): add NCBI gene search + sequence retrieval, oligo QC and in-silico PCR verification with recharts graphs

Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data

Add MSA pairwise refinement, new UI components (SmoothLoader, Reveal, CursorGlow, Parallax), rate-limit handling in AIInterpretation

Fix share links, persist wizard jobs, add AI interpretation fallback, animate landing

Add global/local BLAST modes, full-length pairwise alignment view, standalone pairwise tool

feat(docking): Vina full-detail — parse 1.2.7 log (RMSD l.b./u.b., version, seed), RMSD table + run-config UI (3e)

feat(uniprot,domains): reviewed/organism filters + debounce/fast-path, PROSITE raw-sequence scan UI (3c,3d)

feat(alignment): multi-method MSA (clustalo/muscle/kalign/mafft/tcoffee) with method selector (3b)

feat(alignment): pairwise global/local alignment via BLAST hit 'Align pair' (3a)

feat(md): verified force field/solvent menu (ff14SB/ff15ipq/ff19SB/amberfb15/CHARMM36 x OBC1/OBC2/GBN2) with alanine-dipeptide createSystem startup probe; explicit errors for invalid combos; dynamic frontend menu

fix(blast): honor program/db/max_hits params, accept DNA queries, poll cap 65 min

feat(md): clay simulation-parameter controls (force field, solvent, run length)

fix(md): reflect OXT across C-CA axis so GBSA stops NaNing on Linux CPU

fix(blast): handle NCBI server overload gracefully

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: UniProt fallback search by protein name when NCBI mapping fails

feat: Gemini fallback for AI interpretation when Groq fails

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

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

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

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: wrap sequence/length under query key for frontend AssembledContext

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