fix: replace broken PDBe embed URL with Mol* viewer (molstar.org)

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

fix: replace dead embed.rcsb.org iframe with PDBe Mol* viewer

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

refactor: enhance dashboard with quick tools, jobs with filter tabs, settings with profile identity

fix: default import PhyloTreeViewer in alignment, report, and PipelineResults

feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

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

fix: use embed.rcsb.org instead of www.rcsb.org for clean 3D viewer iframe

feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components

feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation

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

Security, crash fixes, demo prep, dead code removal

Fix structure viewer iframe: embed.rcsb.org is dead → use www.rcsb.org/3d-view/{pdbId}

Fix: alignment sample sequences, reverse complement tool, BLAST program filtering, sample buttons on structure/pathway pages

Fix Phase 1 endpoints: resolve UniProt→PDB in structure viewer, use proper Reactome search, surface real backend errors in frontend

Polish: restyle blast/dashboard/jobs/history/results pages to dark theme, fix Loader2 icons, update result components

Guest upgrade, DB migration, settings functional, full Phase 1 feature set

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

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

fix: remove Lenis SmoothScrollProvider - blocks native scroll in dashboard layout

fix: animate='visible' -> animate='show' to match fadeUp variant

fix: rename lucide-react icons (LoaderCircle, CircleCheck), remove unused imports, replace Set.isSubsetOf

fix: dark input/textarea/select backgrounds and focus border override

full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus

redesign: BioFlow AI void-dark theme — new landing page, dashboard, Three.js DNA helix, Lenis smooth scroll

dark mode: add missing CSS overrides (gradients, forms, badges, hover, bg-opacity, teal variants) + ThemeToggle on landing, auth, callback, shared pages

settings: mark notifications & danger zone as coming-soon, clean up unused state/imports

named exports, any->unknown, theme toggle (light/dark), dark mode fixes, error extractor, deleted pipline/ typo dir

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

fix: Analyze button on retrieve page + sessionStorage handoff to blast wizard

fix: E-value underflow, AlphaFold step, steps_completed append, UniProt always runs

fix: use Array.from instead of Set spread for TS compatibility

fix: FASTA header text bleeding into sequence validation, add IUPAC codes U O B Z X J

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

Re-enable OAuth: restore auth pages, Providers wrapper, dashboard auth guard, landing page CTA

AlphaFold 3D viewer via 3Dmol.js — pLDDT confidence coloring, style selector, spin toggle

Core pipeline testability: progress callback, rate limiter 429, history table

Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)