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

fix: switch runCastp to longApi (660s timeout)

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

fix: retry NGS run on 503 (Render cold start)

fix(ngs): dynamic locus + SAM-first igv.js for reliable genome browser

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

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

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): send alignment_mode from wizard to pipeline v2 API

fix(function-predict): add BP term, real AA composition, JSON export, UniProt distinction, and /learn topic

fix(pathways): read enrichment results from projection response, add p-value and gene ratio

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

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

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

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

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

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

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

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

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

fix: OpenMM via micromamba + BioPython structural fallback, real error messages

feat: scientifically accurate MD simulation with OBC2 solvent, Kabsch RMSD, per-residue RMSF

Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

Phase 0a: SSRF protection + auth on docking/sequencing, worker design doc

Docking viewer upgrade: Molstar GPU rendering, proper interaction geometry, 3D dashed-line rendering

Fix docking route mismatches: GET /status/{id}, frontend pdb URL prefix

feat: add interaction fingerprinting and 3Dmol.js viewer to molecular docking page

feat: add query coverage, organism, and query accession to BLAST results

feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

feat: implement 8 tool bridges (F1-F8) + audit child components

Phase 3: Sequencing pipeline (FASTQ -> QC -> alignment -> variant calling -> report)

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update

feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)

Security, crash fixes, demo prep, dead code removal

Sprint 3-7: Alignment, Structure Viewer, Pathway Analysis, Utility Tools, analyze page fully live

Sprint 1-2: JWT auth middleware + UniProt dedicated page

design.md + rules.md compliance: dark theme, teal palette, pulsing dot, Pydantic models, api.ts routing, config fixes, db/max_hits threading, Supabase migration 004

Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow