Moleculogic System Manual · v3.12

The operating system for preclinical translation.

Moleculogic unifies molecular design, virtual wet lab falsification, decentralized verified compute, SEI regulatory interpretation, and collaborative deal-room packaging into one closed-loop MetalDrug workspace.

01
Design
Encode therapeutic logic as programmable blueprints.
02
Falsify
Destroy non-viable designs before synthesis.
03
Compute
Run ADMET, docking, dynamics, and screens.
04
Interpret
Convert raw outputs into SEI regulatory reasoning.
05
Package
Move evidence into IND and eCTD deal rooms.

From isolated CADD to a verified preclinical-to-regulatory machine.

Traditional computer-aided drug design platforms are often isolated from verification, regulatory packaging, and evidence governance. Moleculogic closes that gap by treating each compound as a causal architecture, not a static formula. The platform is designed to eliminate non-viable molecular trajectories digitally before chemical synthesis, then carry surviving evidence into verified compute and regulatory packaging.

Layer 01

Molecular Design Layer

Programmable Therapeutics

The first stage defines the compound's causal architecture. In Moleculogic, a drug is treated as a programmable state-machine designed to execute conditional therapeutic behavior.

Visual Canvas
Moleculogic Navigator

A node-based canvas where non-technical researchers map metal, trigger, linker, payload, and function nodes into a machine-readable blueprint.

  • Drag metal, trigger, and function nodes.
  • Connect directional therapeutic logic.
  • Compile into standardized JSON blueprint memory.
Architecture Builder
FDC Designer

Configures multi-component drug complexes by scaffold, targeting layer, linker system, payload behavior, and delivery environment.

  • Select scaffold and transport vehicle.
  • Define targeting moiety and linker chemistry.
  • Run compatibility checks before compilation.
Metal Core
MDC Blueprint Builder

Programs metal-centered coordination chemistry, oxidation state, ligand exchange behavior, geometry, and activation thresholds.

  • Select Ru, Pt, Cu, Zn, or other core.
  • Set geometry and oxidation state.
  • Configure exposure and receptor activation logic.
Layer 02

Virtual Wet Lab

Pre-Synthesis Validation

The Virtual Wet Lab is a pre-synthesis contradiction and constraint engine. It is not positioned as a replacement for physical assays. Its job is to find biological, chemical, and regulatory failure modes before capital-intensive experiments begin.

Contradiction
Causal Contradiction Engine

Checks blueprints against biological rules and pathway compensation risks. Contradictions become FLAG_VIOLATION records that block promotion.

Geometry
Topological Pocket Encoder

Vectorizes binding pockets using persistent homology and compares candidate conformers against target pocket topology.

ADMET
Info-Theoretic Validation

Compares simulated pharmacokinetic distributions against empirical compound-class behavior to detect optimism bias.

Clinical Feedback
Failure-State Reintegration Engine

Harvests real-world clinical failure modes and reintegrates them as tighter design constraints for active blueprint scoring.

Output
Promotion Decision

Blueprints advance only when contradictions, toxicity flags, and evidence gaps are visible and bounded.

Layer 03

Secure Compute Layer

ExergyNet Verified

The secure compute layer dispatches heavier workloads to ExergyNet, a decentralized peer-to-peer prover swarm. The user sees a predictable quote and a verification receipt. The backend handles job packaging, escrow, prover execution, result reconciliation, hash checks, and settlement.

Input
Blueprint, Upload, or SMILES

Pull from the ledger, upload SDF/PDB/SMI/MOL2/JSON, or paste a validated chemical string.

Quote
Dynamic Pricing

The pricing oracle estimates cost by molecule size, compute class, and gate complexity.

Run
Prover Execution

A randomized node executes ADMET, dynamics, package compiling, or encrypted screening workloads.

Verify
ZK Receipt

Input hash, output hash, node signature, proof hash, and settlement record are reconciled.

// Result Verification Loop
User job → MetalDrug package → ExergyNet dispatch → Prover swarm execution
→ Secure result sump → Local hash reconciliation → On-chain proof check
→ ZK-verified result → SEI interpretation → Deal room attachment
Layer 04

SEI Regulatory Interpretation

Evidence to Meaning

SEI is the cognitive bridge between computed data and human regulatory affairs. It binds the active blueprint, verified database values, regulatory context, and document needs into a constrained interpretation layer.

AskMo Workspace

A stateful copilot that reads the active blueprint context and explains mechanism logic, drug-drug interaction risks, evidence gaps, and package needs without inventing values outside the database context.

FDA 7-Step Credibility

A model-risk calculator that maps model influence and decision consequence into risk category, validation burden, and NAM requirements.

  • Regulatory toggle constrains the workspace to FDA, ICH, and NAM-oriented reasoning.
  • SEI identifies missing validation steps such as hERG patch clamp, metabolic stability, cytotoxicity, or tissue-on-chip assays.
  • Every interpretation should preserve the boundary between hypothesis, compute result, experimental evidence, and regulatory conclusion.
Layer 05

Regulatory Deal Rooms

Compile and Lock

The packaging layer turns validated simulations and SEI interpretation into collaborative IND and eCTD workflows. Rooms are organized by FDA gates, role permissions, document state, and attached compute evidence.

Roles
Controlled Collaboration

Invite owners, editors, auditors, and viewers with clear document permissions.

Guard
Active Logic Guard

Commit-time parsing blocks or flags values that contradict the active blueprint safety limits or verified compute outputs.

Evidence
Compute Attachment

Attach ExergyNet simulation results directly into nonclinical, CMC, FDA meeting, and evidence appendix documents.

// Deal Room Output
Validated documents → cEIP proof cards → release workflow → eCTD export package
→ FDA ESG-ready zip structure → audit history and provenance trail

Design the molecule. Audit the logic. Verify the compute. Package the evidence.

01
Build Blueprint

Use Navigator, FDC Designer, or MDC Builder to define the therapeutic state machine.

02
Run Virtual Wet Lab

Detect contradictions, topology mismatch, ADMET divergence, and clinical failure analogs.

03
Launch Secure Compute

Run verified ADMET, dynamics, docking, screening, or IND compiler jobs through ExergyNet.

04
Interpret and Package

Use SEI to convert outputs into regulatory meaning, then attach evidence to deal room documents.

Start with a blueprint, a target, or a regulatory problem.

MetalDrug can route the inquiry into molecular design, virtual wet lab validation, ExergyNet compute, SEI regulatory interpretation, or deal room packaging.