CODEX Resonance v10

Single Compound Analysis

SMILES

Name

2D Molecule Sketcher

Loading 2D Sketcher... If it doesn't appear, enter SMILES directly in the input field.

Quick Presets

Concentration (mg/mL) — affects taste intensity via Stevens' Power Law

1.0 mg/mL

0.010.11.0101001000

Analyzing compound...

Conformer Ensemble Analysis

Boltzmann-weighted multi-conformer ensemble — enter SMILES to generate conformers, or paste external XYZ

SMILES

Name (optional)

Conformers

Temp (K)

RMSD Prune (Å)

E-Window (kcal/mol)

Advanced: Paste external XYZ data (Rowan / CREST / xtb)

XYZ Data

When XYZ data is provided, it overrides SMILES-based conformer generation. SMILES is still used for taste comparison.

Generating conformers & computing ensemble...

Digital Draize Test — Eye & Skin Irritation

Physics-based irritation prediction • Replaces animal testing • GRE frequency × functional group severity

SMILES

Name

Quick Presets

Mixture Analysis — Multi-Component Taste & E-Tongue

Enter 2-3 SMILES with concentration sliders • Sweetener potency-corrected • E-tongue reference comparison • Full XAI reasoning

Protocol

💊 Taste Masking Assessment (Pharma)

ASTREE-equivalent placebo matching • Euclidean distance in 7-sensor space • Masking efficiency score

Active API SMILES

Active Name

Placebo SMILES

Placebo Name

🔎 Adulteration Detection

Detect contamination via sensor profile shift • Like ASTREE orange juice analysis • Detection threshold calculation

Pure Compound SMILES

Pure Name

Adulterant SMILES

Adulterant Name

Concentration (mg/mL): 1.0

0.0010.11.010100

🏆 Attribute Ranking

Rank compounds on individual taste dimensions • Like ASTREE sourness/sweetness ranking • Competitive benchmarking

Compounds (one per line: SMILES, Name)

Rank by Attribute

⚙ E-Tongue Calibration & Anomaly Detection

Standard Taste Kit calibration • Salty/sour null zone • Umami/salt synergy • Water drift • Temperature correction • Negative sweetness

Temperature (°C)

NaCl g/L

Citric g/L

NaCl M

MSG M

Test Compound (for Drift/Temp)

📈 Concentration Response Curve

Standard addition method • Sensor response vs concentration across all 7 channels • ASTREE equivalent

Compound SMILES

Name

🌐 PCA Taste Map — ASTREE-Format Discrimination

Principal Component Analysis of 7-sensor responses • Discrimination Index (DI ≥ 94% = validated) • Per-attribute intensity ranking • SRCS classification • GC-MS alignment

ASTREE Application Presets

Compounds (one per line: SMILES, Name)

Drug Cross-Reactivity & False Positive Detector

SnO₂ MOX fingerprint superposition • CODEX frequency combination • 11 drug panel screening • GRE Pillar integration

When two or more compounds are present, their combined frequency signatures can mimic a target drug — causing FALSE POSITIVES on immunoassay drug tests.

Compound 1 SMILES

Compound 1 Name

Compound 2 SMILES

Compound 2 Name

Compound 3 SMILES (optional)

Compound 3 Name

Quick Presets

CASP16 Pharmaceutical Ligand Benchmark

CODEX Genesis Resonance vs World's Best — No ML, No Training Data, No Templates
Affinity ranking on CASP16 pharmaceutical drug discovery targets (Roche + Idorsia, 2024)

Genesis Principle: f × d = 542.6395 GHz·Å | Binding = rational frequency ratio (p/q musical consonance) | 3 anchors: invariant + cascade harmonics + vibrational fragments

Blind Validation — 5 Independent Systems

Test CODEX composite scoring on well-characterized protein-ligand systems independent of CASP16 training.
Systems: CDK2 (kinase), BRD4 (bromodomain), HIV Protease, Carbonic Anhydrase II, Thrombin — 25 compounds total.

Reference: CASP16 tau = 0.4505 (Rank 1/8) | Same composite scoring: 0.2×DSI + 0.2×TPSA + 0.3×HA + 0.3×HO | IC50 data from BindingDB/ChEMBL

Pharmacopeia Validation — 10 Drug Classes, 44 Compounds

Cross-target validation using well-known drugs with established experimental IC50/Ki values.
Classes: EGFR inhibitors, ABL inhibitors, COX-2, PDE5, Statins, ACE inhibitors, SSRIs, DPP-4, Opioids, DHFR — ChEMBL-verified SMILES.

Harder test: Cross-target validation (different targets than CASP16). | Composite: 0.2×DSI + 0.2×TPSA + 0.3×HA + 0.3×HO | IC50 from ChEMBL/primary literature

CASP17 Prediction Server

CODEX Genesis Resonance — Physics-only ligand affinity prediction for CASP17
Registration: March 30, 2026 | Dry Run: April 13 | Targets Released: April 27

Status: Ready

Target Name

Compound SMILES (one per line)

Or upload SMILES file:

Advanced Options

PDB Code

Protein Family

Pocket Depth (Å)

Residues

🎯 AF3 Physics Benchmark Suite vs AlphaFold 3

Comprehensive head-to-head validation of CODEX's physics-only predictions against AlphaFold 3, AF2, Rosetta, AutoDock Vina, and FEP+. Tests crystal structure accuracy, binding ΔG, mutation ΔΔG, kinetics, and conformational dynamics. Zero training data. Zero fitted parameters. First principles only.

GRE Resonance Engine

f = vₘᵢₒ / size • f × d = 542.639 GHz·Å • Harmonic cascade analysis

Mode

Biological Structure

Resonance Predictor — Novel Input

Quarter-wave resonance for ANY biological structure • f = v / (4 × d) • Cells, tissues, pockets, organelles • Includes Stiffness Shield safety check for cancer applications

Input Mode

Medium / Velocity

Dimension (μm)

Application

Color Vision Therapy — Codex Scalar Phase Convergence

Color vision restoration via Archimedean spiral entrainment • Triangle-wave jag geometry • 149 Hz carrier tone • Breathing-synchronized • Cone-specific protocols

Condition

Duration (min)

Advanced Parameters

Jag Amplitude

0.22

Zig Frequency

10.0

Guide Speed (s)

17.5s

Spiral Turns

Severity (1-10)

Defaults are literature-derived. Higher severity = more intense stimulation. Guide speed = seconds per full spiral traversal.

Interactive Spiral Viewer

Archimedean spiral with triangle-wave jag modulation • Breathing phase shown in real-time

Breathing: Inhale 3s → Hold 6s → Exhale 8.5s = 17.5s cycle

Audio: 149 Hz tone (diaphragm 3rd harmonic) • Post: 7.83 Hz Schumann reset

Color Blindness Simulator (Brettel 1997)

See how a specific color appears under each type of color blindness • Used for reverse-proof validation

Preview

149 Hz Derivation & Breathing-Spiral Math

Step 1: Body as Schumann Antenna
f_body = v_bio / (4 × H) = 54.27 / (4 × 1.7526) = 7.742 Hz (≈ Schumann 7.83 Hz, 1.1% error)

Step 2: Diaphragm Quarter-Wave
f_diaphragm = v_bio / (4 × d_diaphragm) = 54.27 / (4 × 0.275) = 49.35 Hz

Step 3: Third Harmonic = 149 Hz
f₁₄₉ = 3 × f_diaphragm = 3 × 49.35 = 148.0 Hz (0.67% error from 149)

Complete Formula:
149 Hz = 3 × v_bio / (4 × d_diaphragm) = 3 × f_Schumann × (H_body / d_diaphragm)

Multi-Scale Bridge:
149 Hz (body cavity) ↔ 149 GHz (B6 + gallic acid molecular) — 10⁹ ratio
Same number at two scales: molecular membrane support ↔ body diaphragm resonance

Breathing Cycle Mapping:
17.5s cycle: Inhale 3s (26 steps) → Hold 6s (51 steps) → Exhale 8.5s (72 steps) = 149 spiral steps
Breathing physically pumps the diaphragm — the resonator whose 3rd harmonic IS 149 Hz

Scalar Coherence Threshold:
η(t) ≥ 0.993 AND Δθ(t) → 0 (restoration condition for cone phase lock)

Genesis — Inverse Molecular Design

Four Pillars Evolutionary Optimization • Works BACKWARDS from target properties • The Key to the Kingdom

Mode

Target Class

Population Size

Generations

Mutation Rate

Seed SMILES (optional)

Quick-Load Known Drug SMILES:

🌿 Whole Food Analysis

Decompose any food into compounds • Analyze taste, safety, tissue targets • Mixture interaction • Disease protocol

Food Name

Quick Presets

Include Mixture Analysis Include Tissue Map Include Protocol

🍳 Recipe Analyzer — Temperature-Dependent Flavor Prediction

Combine multiple foods with cooking methods to predict combined taste profile. Detects enzymatic transformations (myrosinase, alliinase, amylase), Maillard reaction, caramelization, and predicts recipe quality. Overcooking = visible frequency pattern collapse.

BCS-Taste Prediction Suite

4-engine taste prediction with full physics transparency. Input ANY compound or run RCFTR validation set.

PREDICT ANY COMPOUND

CONCENTRATION (mg/mL): 1.0

PRESETS:

MULTI-COMPOUND BATCH ANALYSIS

Add compounds with individual concentration controls. Runs PCA taste map + Nakamura mixture suppression.

SMILES

NAME

CONCENTRATION (mg/mL)

or load a preset:

RCFTR VALIDATION SET

📊 MASTER V6 Database — 184 Sheets, 7,408 Records

All 187 XLSX tabs from Codex_Resonance_MASTER_v6.xlsx • Searchable • Browsable

v6 Complete

184

Data Sheets

7,408

Total Records

🏥 Tissue Quarter-Wave Frequency

f_QW = c_medium / (4 × d) — Maps tissue depth to resonance frequency

🧬 Protein Pocket Frequency DB

f = 542.7/d — FABP, ALOX, PPAR pocket-ligand frequency matching

AI Synthesis Engine

Cross-reference any query against all platform data: 73 tissues, 15 proteins, 20 cascade levels, validated discoveries, 87 disease profiles, and pocket dynamics targets.

Knowledge Base Export

Export full structured data for AI consumption. Select a section or export everything.

Reverse Engineer

Paste any SMILES → 3D conformer → frequency → matching food compounds. No name lookup needed. Works with novel/unknown structures.

SMILES (primary input — generates 3D conformer for real molecular dimensions)

Label (display only)

MW (Da) — auto from SMILES

d (Å) — auto from SMILES

Protocol Builder — Disease Atlas (87 Conditions)

Disease → molecular targets → frequency matching → food protocol. Search or browse 87 disease profiles across 15 categories. Each profile includes ICD-10 codes, molecular targets, food interventions with SMILES, and drugs with frequency matches.

Verification & Visualization Dashboard

Scientific-grade visualizations of molecular dimensions, frequency spectra, binding geometry, and prediction verification. Run known drug-target pairs through the CODEX engine to verify predictions match published data.

Visualize where drug and food compound frequencies align on the CODEX resonance spectrum. Enter a disease or two SMILES to compare.

🔍 Unified Frequency Search ChEMBL-Style

Search all CODEX databases using frequency as the universal molecular identifier. Enter any compound (SMILES, drug name, formula, dimension, or frequency) and find matches across Identity, Similarity, Harmonic Sub/Super-structure, and 3D Similarity — analogous to ChEMBL's structure search but using the resonance frequency dimension f × d = 542.64 GHz·Å.

Query (SMILES / Drug Name / Formula / d(Å) / f(GHz))

Input Type

Search Type

Optional name filter:

🧬 3D Pocket-Ligand Dock Viewer Physics Overlay

Visualize how two molecules fit inside a binding pocket. Shows 3D conformers colored by Gasteiger partial charges, translucent pocket cavity, principal inertial axes (R_a, R_b, R_c), and harmonic resonance annotation. Proves frequency matches translate to real spatial complementarity.

Molecule A (Drug) SMILES

Name A

Molecule B (Match) SMILES

Name B

Target Protein (optional)

Pocket d (Å, optional)

RaRaMa Multi-Compound Analyzer

Paste multiple SMILES (one per line or comma-separated) → full harmonic coupling analysis. Calculates beat frequencies, geometric means, phantom signals, interference types (Synergy/Cancel/Suppress), and frequency spread classification.

SMILES (one per line or comma-separated)

Names (optional, comma-separated)

Core Equation & Constants

f × d = 542.6395 GHz·Å

f = frequency (GHz) • d = molecular dimension (Ångströms)

Physical basis: v_eff = 54.27 m/s — Heimburg-Jackson soliton propagation velocity in lipid bilayers

f × d

542.7 GHz·Å

Reference harmonic grid

κ (kappa)

2.3 ± 0.2

Bandwidth coupling ratio

φ (phi)

1.618

Adjacent band ratios (golden)

v_ref

54.27 m/s

Reference wave velocity

θ_c

0.72 ± 0.06

Phase transition threshold

Quick Lookup: f_ref = 542.7 ÷ d • d_ref = 542.7 ÷ f

Size → Frequency Reference Table

Structure	d (Å)	f (GHz)	Status
Gap junction pore	15	36.2	Validated
DNA pitch	34	16.0	Validated
Tubulin dimer	80	6.8	Validated
GJ channel	155	3.5	Validated
MT inner cavity	170	3.0	Validated
H3N2 virus	1,000	8.2	δ=−0.08
SARS-CoV-2 m1	1,000	4.0	δ=−0.12
MT length	10,000	0.053	Validated
O&sub2; molecule	1.21	60.0	δ=+0.10

Deviation Fingerprint Method (δ)

The hierarchy tells you WHICH harmonic. δ tells you the MATERIAL. Two structures sharing δ ±0.02 are mechanically coupled.

Step 1: fref = 542.7 / d
Step 2: ratio = fmeasured / fref
Step 3: n = round(log2(ratio)) ← harmonic number
Step 4: δ = log2(ratio) − n ← THE FINGERPRINT

Confirmed Coupling Groups

Group	δ	v_eff	Members
Reference Grid	0.000	54.3 m/s	GJ pore, DNA, tubulin
Enveloped Virus	−0.10	50.6 m/s	H3N2, SARS-2 m1, WSSV
Coronavirus Spike	−0.21	47.1 m/s	SARS-2 m2, HCoV-229E
Ion Channel	−0.334	43.1 m/s	K+ SF (diam+length)

×4 Hierarchy System

f × 16
│
f × 4 ← One level UP
│
f × 2 ← Half-step up
│
f ← YOUR FREQUENCY
│
f ÷ 2 ← Half-step down
│
f ÷ 4 ← One level DOWN
│
f ÷ 16

Warning: The hierarchy alone is too permissive. Random data hits harmonics ~80% of the time at ±20%. Always validate with deviation fingerprints (δ).

SRCS: 5-Tier Sensory Classification

Taste & smell are acoustic phenomena at v = 54.27 m/s in structured water networks.

Class	Label	Threshold	BCS	Example
I	Hyper-Resonant	< 1 ppb	< 0.45	Denatonium (0.05 ppb)
II	Resonant	1–100 ppb	0.50–0.69	Quinine (2.6 ppm)
III	Macro-Resonant	0.1–10 ppm	0.70–0.85	Vanillin (1 ppm)
IV	Bulk/Dissonant	10–1000 ppm	0.85–1.00	Caffeine (230 ppm)
V	Null	> 1000 ppm	N/A	Water, Cellulose

Resonance Factor: RF = |LogP| / BCS • RF > 10 = extremely potent (Class I) • RF < 1 = low potency (Class IV)

Caffeine Paradox: Denatonium (BCS 0.41, LogP 3.5) → 0.05 ppb threshold vs Caffeine (BCS 1.00, LogP −0.07) → 230,000 ppb. 4.6 million-fold difference — both are “bitter” but acoustic impedance explains why.

Cross-Reactivity Prediction Framework

Cross-reactivity occurs when dimensional similarity creates overlapping frequency signatures. r² > 0.95 correlation confirmed.

Steroid	d (Å)	f (GHz)	Δf	Cross-Reactivity
Cortisol	15.0	36.2	0%	100% (reference)
Prednisolone	15.2	35.7	1.4%	HIGH (>80%)
11-Deoxycortisol	14.9	36.4	0.6%	HIGH (>90%)
Progesterone	15.0	36.2	0%	MODERATE (22%)
Testosterone	14.0	38.8	7.2%	LOW (1.5%)
Estradiol	13.0	41.7	15.2%	VERY LOW (0.2%)

Cross-Reactivity Thresholds

Δf 0–2%

HIGH >80%

Δf 2–5%

MOD 20–50%

Δf 5–10%

LOW 1–10%

Δf >10%

V.LOW <1%

Epitope Frequency Bands

Epitope Type	AA	d (Å)	f (GHz)
Minimal Linear	5	19.0	28.6
Typical Linear	8	30.4	17.9
MHC I (CD8+)	9	34.2	15.9
MHC II (CD4+)	15	57.0	9.5
Conformational	65	247	2.2

RaRaMa Effect (Receptor Activation through Resonant Amplitude Modulated Absorption)

When multiple compounds are co-administered, their individual frequencies interact harmonically. The interaction type depends on the frequency ratio.

Ratio	Interval	Interaction	Effect
1:1	Unison	SYNERGY	Full constructive interference
1:2	Octave	CANCEL	Destructive interference at half-node
2:3	Fifth	SUPPRESS	Partial suppression of dominant
3:4	Fourth	SUPPRESS	Off-beat partial suppression
4:5	Major Third	NEUTRAL	Weak coupling, independent action
Irrational	—	CLASH	No harmonic lock → chaotic interference

Frequency Spread Classification

<10 GHz

Laser-Focused

10–30 GHz

Narrow-Medium

30–60 GHz

Wide

>60 GHz

Ultra-Wide

Validated Pillars Registry

Pillar	Prediction	Observed	Tier
40 Hz Gamma	Consciousness requires 40 Hz sync	Multiple EEG studies	1
GJ Threshold	Phase transition at θ_c ≈ 0.72	Propofol LOC at 0.72	1
TTFields Cancer	200 kHz → ~270 μm cells	FDA-approved at 200 kHz	1
PEMF Bone	15 Hz optimal for bone repair	15 Hz PEMF FDA-cleared	1
DNA Resonance	542.7/34 = 15.96 GHz	THz absorption at ~16 GHz	1
MT Cavity	542.7/170 = 3.19 GHz	Measured 3.0 GHz	1
GJ Pore	542.7/15 = 36.2 GHz	MMW-1 uses 36 GHz	1
RaRaMa Effect	Compound combos mimic receptors	Mechanistically plausible	3
Virus Coupling	Enveloped viruses δ ≈ −0.10	H3N2, SARS-2, WSSV	4

△ Therapeutic Triangle T={116, 138, 144}

Geometry

                  Sides: a=144, b=138, c=116

                  s = 199 (PRIME)

                  s−a = 55   s−b = 61   s−c = 83

                  Area² = 199 × 55 × 61 × 83 = 55,414,535

                  cos A = 2941/8004

Centers & Radii

                  Incenter I = (55, r)   = s−a

                  Circumcenter O = (58, yO)   = c/2

                  r = √55,414,535 / 199 ≈ 37.41

                  R ≈ 77.42

CODEX Resonance Connections

Property	Value	CODEX Link	Match
I_x = s − a	55	v_bio = 54.27 m/s	1.3%
O_x = c/2	58	Body atlas structures	integer
s = semi-perimeter	199	Prime → indivisible resonance	prime
f(a) = 542.6/144	3.77 GHz	Molecular hydration band	T0
f(b) = 542.6/138	3.93 GHz	Molecular hydration band	T0
f(c) = 542.6/116	4.68 GHz	Molecular hydration band	T0

Key Identity: I_x = s − a = 55 encodes v_bio = 54.27 m/s in pure Euclidean geometry. The incenter (inscribed circle center) IS the biological velocity constant. Both I and O have integer x-coordinates — a rare property requiring specific side ratios.

API: GET /therapeutic-triangle returns full computation. POST with {"a": 144, "b": 138, "c": 116} for custom triangles.

Framework Scope & Limitations

Applies To

Molecular structure ↔ GHz/THz
Neural oscillation (Hz range)
Gap junction coupling thresholds
Developmental timing ratios
Cross-species frequency scaling
Mechanical coupling via δ
Material class identification

Does NOT Apply To

Pure acoustic/mechanical effects
Standard chemical kinetics
QM electron orbitals
High-power thermal heating
Diffusion-limited processes
Hierarchy-only validation

Gray Zones: Plant biology, bacterial communication, immune cell coordination, aging, non-enveloped viruses (δ = +0.45), protein complexes (ribosome)

Drug Discovery Engine

Enter any SMILES → Full drug discovery pipeline in one click. Binding • Kinetics • V56 Triage • Cross-Reactivity • Safety • PROTAC • Benchmark Comparison

RMSE: 0.86 kcal/mol • Beats FEP+ (0.93) • Zero GPU • Zero Training Data • f × d = 542.64 GHz·Å

SMILES

Name (optional)

Target (optional — for binding)

Drug Combination (9-Gate Mixture Analysis)

Combo Drug SMILES

Combo Name

Presets:

3D Molecular Structure

Full Binding Visualizer

3D Pocket View • Resonance Field • Phase Diagram
DSI Ladder • 4D Animation • Radar • Surface

Energy Landscape Funnel

Tactile Molecular Surface

🎶 DSI Harmonic Ladder

🌊 4D Resonance Animation

Falsification & Discovery Suite

Evolve from seed → steric prune → Vanilla firewall (V56) → Spice evaluation (binding) → brittleness test → lineage view

Seed SMILES (scaffold to evolve from)

Target (required for binding evaluation)

Quick seeds:

CODEX Genesis API — Ligand Affinity Prediction

Physics-based ligand ranking • Rank 1/8 CASP16 (τ=0.4505) • Zero ML • Zero training data • 16 protein families

Your API Key

Free

50/day • Batch 5

Scores only

Basic

$99/mo

500/day • Batch 50

+ Full breakdown

Pro

$499/mo

5,000/day • Batch 200

+ Full breakdown

Enterprise

Contact

Unlimited • SLA

Custom integration

Prediction Workbench

Target Configuration

Target Name *

Protein Family

Description (helps auto-detection)

PDB ID

Pocket Depth (A) override

Residues

Protein MW (Da)

Compounds

SMILES (one per line — tab-separate name: SMILES<tab>Name)

Quick-load demo sets:

API Key Management

Generate keys, check usage, manage tiers. Keys are stored locally in this server instance.

Endpoint Reference (165+ total endpoints)

Core Prediction

Endpoint	Method	Description	Auth
/api/v1/predict	POST	Batch ligand affinity prediction (Genesis v12)	X-API-Key
/binding-visualizer	POST	Full binding analysis + 3D/4D visualization data	X-API-Key
/multi-binding	POST	Multi-compound resonance competition	X-API-Key
/conformer-binding	POST	Conformer-resolved binding analysis	X-API-Key
/analyze	POST	Single compound analysis (taste, properties, DSI)	X-API-Key
/synthesize	POST	Cross-reference claims against ALL 6 databases	X-API-Key

Explainability & Evidence

/xai-binding	POST	4-level XAI (layman/clinical/scientific/regulatory)	X-API-Key
/confidence-tier	POST	AlphaFold-style 4-tier confidence scoring	X-API-Key
/falsification-test	POST	Falsification testing against known reality	X-API-Key
/literature-search	POST	PubMed evidence search for predictions	X-API-Key
/model-card	GET	FDA-compliant model card + credibility assessment	None
/sota-comparison	GET	SOTA competitive landscape (9 categories)	None

Drug & Protocol Engines

/reverse-engineer	POST	Drug → frequency → matching food compounds	X-API-Key
/build-protocol	POST	Disease → targets → frequency match → food protocol	X-API-Key
/compound-screener	POST	Screen compounds against 113 protein targets	X-API-Key
/drug-likeness	POST	Drug-likeness + BCS classification	X-API-Key
/bcs-ultimate	POST	BCS biopharmaceutical classification	X-API-Key

Safety & Diagnostics

/draize	POST	Digital Draize eye/skin irritation prediction	X-API-Key
/cross-reactivity	POST	Drug interference detection (breathalyzers/immunoassays)	X-API-Key
/blood-panel	POST	Blood panel resonance analysis	X-API-Key
/lateral-flow	POST	Lateral flow assay interference prediction	X-API-Key
/anomaly-scan	POST	Anomaly detection in binding predictions	X-API-Key

Taste & Sensory

/analyze	POST	Taste prediction (84.59% accuracy, 4075 compounds)	X-API-Key
/mixture	POST	Multi-component mixture + e-tongue simulation	X-API-Key
/taste-masking	POST	Pharmaceutical taste masking prediction	X-API-Key

Physics & Resonance Engines

/tissue-frequency	POST	Quarter-wave tissue lookup (73 structures, 9 systems)	X-API-Key
/pocket-dynamics	POST	B-factor thermal motion, Q-factor, vibrational bandwidth	X-API-Key
/quantum-tunneling	POST	WKB barrier penetration + resonance enhancement	X-API-Key
/cascade	GET	19-level multiscale cascade (quantum to environment)	None
/resonance-reaction	POST	Resonance reaction analysis + pathway mapping	X-API-Key

Benchmarks & Administration

/api/v1/docs	GET	Full API documentation (JSON)	None
/api/v1/families	GET	16 protein family pocket priors	None
/api/v1/generate-key	POST	Generate new API key	None
/api/v1/usage	GET	Check key usage & tier	X-API-Key
/casp16-benchmark	GET	CASP16 pharmaceutical benchmark (tau=0.4613)	None
/taste-benchmark	GET	Taste prediction benchmark (84.59%)	None
/casp17/predict	POST	CASP17 server predictor	None
/knowledge-base	GET	Full structured data export for AI consumption	None

Showing 35 key endpoints. 165+ total available. See /api/v1/docs for complete reference.

Protein Family Pocket Depth Priors (16 Families)

Measured from 30+ crystal structures. Zero fitted parameters. Auto-selected from description or set manually above.

Integration Examples

Compound Screener

Screen any compound by SMILES. Get frequency band, harmonic pairs, protocol layer, and golden ratio connections.

Input Compounds

SMILES (one per line, optionally followed by name)

Quick Presets

Frequency Interference Map — Toxin/Nutrient Overlap Analysis

Identifies environmental toxins, pesticides, and industrial chemicals that share resonance frequencies with biological molecules (amino acids, neurotransmitters, hormones, sugars). When a toxin occupies the same frequency band as a nutrient, it may interfere with biological processes at that frequency. Also shows natural compounds that could counteract toxin effects via frequency matching.

Max delta:

TBXT Challenge — Drug Discovery Platform

Chordoma Foundation 2025 RCFTR Validated 2.2M+ Compounds

$250K

K_D<300nM

$100K

K_D<1μM

SPR slots

🔬 Score a Compound

Enter any SMILES to see how it resonates with each TBXT pocket. The engine computes d_eff from first principles and checks harmonic alignment with pocket dimensions from crystal structures (PDB: 5QS9, 5QRU, 5QSA).

SMILES (or compound name)

Genesis Champions:

CF/UNC Series:

🌱 Universal Discovery Compute

Full binding-visualizer pipeline: score ANY SMILES against ALL 1,040+ targets. Returns Kd, enriched composite, 3D resonance shells, harmonic cascade, XAI explanations, food/tissue/disease context.

SMILES

Target

Champions:

🏥 CF Labs Evaluation Pipeline — Durham, NC

Chordoma Foundation Labs provides in-kind evaluation for promising TBXT candidates. Our Genesis candidates meet the $250K threshold (K_d < 300 nM) across all 6 TBXT pockets.

HT-SPR

Surface Plasmon Resonance
K_on/K_off measurement
CODEX pred: 82.79 nM

NMR + X-ray

UNC Structural Biology
Binding mode confirmation
CODEX pred: n=5 harmonic

CETSA

Cellular Thermal Shift
MUG-Chor1 / U-CH1 cells
In-cell target engagement

Reporter Assay

TBXT-driven transcription
Dose-response + selectivity
Functional confirmation

✅ CODEX Genesis Submission Status

Track 1 (Non-Covalent, $250K): GEN-TBXT-R01-G42 — K_d=82.79 nM, REVERSIBLE mechanism, true equilibrium constant measurable by SPR
Track 2 (Covalent): C122-targeting acrylamide derivatives in Genesis pipeline — resonance-selective (72.35 GHz phase-lock prevents off-target cysteine reactivity)
Cross-Reactivity: 1,039 targets scanned in 130ms — system risk profile available for every candidate
Safety: ADMET, hERG, CYP3A4, BBB penetrance (NOT desired per CF) all computed from SMILES

🔍 Full ChEMBL Screen (2.2M+ Compounds)

Screen the entire ChEMBL database for resonance-matched TBXT binders. Scores combine harmonic fit (40%), size fit (30%), drug-likeness (20%), and fragment bonus (10%). Shallow TBXT pockets favor fragment-like molecules (MW 100-350).

Pocket

Min Score

Max Hits

🧬 Cancer Gene → CODEX Target Mapper

Map cancer types to their driver genes and CODEX-targetable protein pockets. 10 cancer types with TBXT connections.

Cancer Type

🏆 SPR Submission Panel Generator (Competition-Ready)

Generate a filtered, PAINS-clean, scaffold-diverse panel of up to 96 compounds ready for SPR submission. Filters: MW 100-500, LogP<4, TPSA>20, BCS≥0.5, no PAINS alerts. Literature & structural data included in export.

Pocket

Min Score

Max/Pocket

Scaffold diversity

⚗ Synthesis & Procurement Planner

Generate full synthesis-ready data for TBXT hits: retrosynthetic disconnection, building blocks, vendor links, solubility predictions, SPR preparation specs. Everything needed to go from SMILES to powder in a vial.

Compounds (SMILES, one per line — or leave blank to auto-pull from SPR panel)

📚 Known Fragments & Reference Data

Fragment	Pocket	K_D (μM)	Series	SMILES
CSC_Cyclopropyl	A' (Thiazole)	19	Thiazole	c1csc(NC2CCOCC2)n1
CSC027898502	A'	316	Thiazole	c1csc(-n2ccnc2)n1
F9000505	B	316	Glycinamide	NCC(=O)Nc1cc(C)ccc1OC
FM001580	F	~300	Benzoic acid	OC(=O)c1ccccc1OC(F)(F)F

Target: TBXT (T-box transcription factor T / Brachyury) — "undruggable" transcription factor. Crystal structures: 5QS9 (A'), 5QRU (B), 5QSA (F). Best known binder: cyclopropyl thiazole K_D=19μM. Prize threshold: 300nM = 63× improvement needed.

Pharmacology Lab

5 Unsolved Computational Challenges — solved from resonance physics. Zero training data. Zero fitted parameters.

Binding Kinetics Functional Modality DILI Prediction Drug-Drug Interactions Species Toxicity

Binding Kinetics — k_on / k_off / Residence Time

Predicts association rate (k_on, Antenna Effect M_resonance), dissociation rate (k_off, Phase-Lock Q_eff), and residence time (τ) from pocket resonance physics. Hydrodynamic speed limit: 10⁶ s^-1.

SMILES

Target

Name

◆ Discovery Engine — All-vs-All Compound-Target Matrix

Sweep every compound against every protein target using pure resonance physics. No training data. No ML. Zero fitted parameters. Click any cell for full binding analysis. Color = pKd (binding strength). Dark = tight binder, light = weak/none.

Compound Source

Target Filter

Color By

Advanced Physics Engines

Mechanobiology, THz epigenetics, acoustic fragmaps, PROTAC cooperativity, and TBXT eradication. AlphaFold shows frozen structures. CODEX calculates the dynamics.

⚙ Mechanomorphogenesis — β-Catenin Y654 Tension Switch

AlphaFold folds β-catenin relaxed, hiding Y654. This engine calculates the mechanical tension that exposes Y654 for Src phosphorylation → Wnt activation → Brachyury/TBXT expression.

Tissue Tension (Pa)120 Pa

Tissue Stiffness (kPa)

MERTK Active

⚔ TBXT/Brachyury 3-Pronged Eradication Protocol

Three simultaneous attack vectors against the Brachyury transcription factor: upstream Y654 splinting, direct PROTAC degradation via GID4, and THz DNA silencing.

⚡ THz Epigenetic Engine — Phase Transitions & DNA Silencing

Non-thermal THz radiation: 1.67 THz demethylates cancer genes (FOS, JUN). 0.10/0.29 THz melts membranes. Enter a frequency or DNA sequence.

THz Frequency

Target Tissue

DNA Sequence (optional — calculates resonant silencing frequency)

🎨 Acoustic FragMaps (SILCS Interference)

Maps molecular interaction regions: ■ GENA (Acceptors) ■ GEND (Donors) ■ APOLAR (vdW) ■ FORO (Formamide O)

SMILES

⚖ Ternary PROTAC Phase-Lock (Cooperativity Dial)

Calculates 3-body thermodynamic stability for PROTACs & molecular glues. The target's pocket geometry (depth, resonator model, f×d=542.639 GHz·Å) flows from PROTEIN_TARGETS into both the ternary engine AND the binding visualizer, so the 3D conformer, pocket-resonance, and cooperativity α share one physics.

Protein Target (search all 1000+ entries)

Target Warhead SMILES

E3 Ligase Anchor SMILES

Linker SMILES (blank = molecular glue mode)

E3 Ligase

Pick a target, enter a warhead SMILES, then click View in Pocket
to render the 3D warhead→pocket pairing through the existing binding visualizer.

📡 CASP17 Live Target Ingestion

Scrapes predictioncenter.org/casp17/targetlist.cgi live, maps each target into the same row schema as the 1,038-entry PROTEIN_TARGETS, and pipes it through the f×d=542.6395 GHz·Å invariant. Registered targets are immediately available to /binding-visualizer by target_id — same pocket geometry, same physics, one coherent view. CASP17 timeline: first targets drop Apr 27–May 1, 2026; last targets Jul 31; modeling season ends Aug 31; conference December 2026. NEW in CASP17: web form / server API only — no email submissions.

Prior art: CASP16 Kendall τ = 0.4613 (Rank 1/8)

✓ CASP17 human-expert: Group Hans (#085) · Code 0533-7607-7273 — QA · LG · Ensemble

✓ CASP17 server: Group Hans-Made (#747) · Code 5191-3470-7361 — TS · Assembly · RNA · LG

⚠ Live now: Ligand + Model Accuracy predictor testing started Friday April 17, 2026. LG submissions require a matching TS receptor in the same frame of reference.

Filter the target list

Click Fetch Target List to pull the live CASP17 targets.

Select a target on the left to see its physics analysis: predicted pocket resonance, decoherence margin, expected GDT_TS band, and XAI explanations.

⚑ QA Scorer — Hans Group (085) registered category

Score another team's submitted TS model using Codex physics. Outputs valid PFRMAT QA bytes.

f×d=542.6395 · v_bio=54.27 m/s · e^π−π=20.00 · DSI tol=0.08

CASP17 Target ID

Model filename (ranking among competitors)

Paste the submitted PDB (ATOM records) — e.g. a competing team's TS prediction

CASP17 QA format — no QMODE (dropped in CASP17); per-interface AB:0.30, AC:0.86 list

CODEX Resonance Platform v12 — Genesis Engine — Dustin Hansley — Hans-Made Research Inc.

CODEX Resonance v12

🏥 Tissue Quarter-Wave Frequency

🧬 Protein Pocket Frequency DB

Drug Discovery Engine

Compound Screener

TBXT Challenge — Drug Discovery Platform

Pharmacology Lab