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(seo): JSON-LD structured data — Organization/WebSite graph, SoftwareApplication+HowTo homepage, BreadcrumbList across tools

feat(branding): Synteny rebrand — new identity, signal-coded palette, and pipeline icons

feat(results): in-app share dialog + self-normalized dotplot scoring

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

feat(design): bioluminescent green+violet palette and re-tuned landing hero

feat(ui): apple-design conformance — springs for micro-interactions, reduced-motion/transparency/contrast support, typography tracking

feat(theme): dual light/dark mode with Apple light theme, toggle, and theme-aware viewers

feat(seq-tools): MSA match/mismatch/gap cell highlighting, consensus row and legend

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(alignment): show matched/mismatched/gaps/length stats across all alignment views via shared AlignmentStatsBar

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

feat(export): add downloads to ADMET, MD, pairwise, AlphaFold, docking, pathway, plus 4 new learn topics

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

Fix AI model fallback chain and enrich share message with result details

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

Refine design system: semantic color tokens, tiered motion, denser result cards, VinaLog toolbar

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