Pauling runs the simulations that decide which molecules are worth making -- physics-based docking, full molecular dynamics with MM-PBSA, ADMET, and QC, end-to-end through conversation. A hit optimization pipeline built on REINVENT 4, the same open-source generative engine, also generates novel analogs from validated hits, expanding beyond the commercial catalog. AIDDISON (Merck KGaA / Sigma-Aldrich) is a design-and-search SaaS platform for medicinal chemists: generative de novo design (REINVENT 4.0), 60B+ searchable compounds, and SYNTHIA synthesis planning -- but no MD and no high-throughput physics-based screening.
| Category | Pauling | AIDDISON |
|---|---|---|
| Primary focus | End-to-end simulation: docking, MD, ADMET, QC | Design and search: de novo generation, similarity/shape search |
| De novo design | REINVENT 4 generative design, integrated into the automated hit optimization pipeline | REINVENT 4.0 generative AI -- optimizes QED, ADMET, and affinity |
| Chemical space search | Supplier and owner-scoped catalogs | 60B+ searchable molecules; 25B+ SA-Space make-on-demand compounds |
| Docking | UniDock (GPU-accelerated Vina) -- screens 10M+ compounds | Cresset Flare docking -- interactive, visualization-oriented |
| Molecular dynamics | Full GROMACS MD with auto parameterization, MM-PBSA | Not available |
| ADMET profiling | Integrated into conversational workflow | ML models trained on Merck proprietary R&D data; customizable with your own |
| Synthesis planning | Not available | SYNTHIA retrosynthesis integration -- design to manufacturing |
| Pose quality control | PoseBusters automatic QC on all poses | Visual inspection in Flare |
| Pocket detection | P2Rank (ML-based, automatic) | Flare pocket identification |
| Interface | Conversational AI -- describe what you want in natural language | Web GUI with guided workflows |
| Pricing | Pay-per-compute, no license fees | Enterprise subscription -- contact sales |
| Setup time | Minutes (sign up and run) | Enterprise onboarding |
| Vendor | Purpose-built for drug discovery | Merck KGaA / Sigma-Aldrich reagents and software ecosystem |