Pauling delivers docking, MD, ADMET, and pocket detection through a conversational interface on cloud infrastructure -- no licenses, no tokens, no desktop installation, minutes from signup to first result. Schrodinger is powerful -- Glide and FEP+ are industry gold standards -- but it's $35,000+/year per workstation with token-based licensing and a steep learning curve.
| Category | Pauling | Schrodinger |
|---|---|---|
| Docking engine | UniDock (GPU-accelerated Vina) -- fast, validated scoring | Glide (SP/XP) -- industry-gold-standard pose prediction and enrichment |
| Free energy perturbation | Not yet available | FEP+ -- best-in-class relative binding free energy, widely validated |
| MD simulations | GROMACS with auto ligand parameterization (ACPYPE), checkpoint save/resume | Desmond -- highly optimized, GPU-accelerated, tight Maestro integration |
| ADMET profiling | Integrated into conversational workflow | QikProp -- established ADMET prediction, but separate module |
| Pocket detection | P2Rank (ML-based, automatic) | SiteMap -- physics-based, accurate, requires manual setup |
| Pose quality control | PoseBusters (automatic, physics-based QC) | Visual inspection in Maestro; no automated QC equivalent |
| Cost model | Pay-per-compute, no license fees | $35K+/year per seat; token-based for cloud jobs |
| Licensing | None -- browser-based access | Per-seat or token-based; enterprise negotiations required |
| Interface | Conversational AI -- describe what you want in natural language | Maestro GUI -- powerful but steep learning curve |
| Cloud scaling | Auto-scales to hundreds of workers on Google Cloud Dataflow | LiveDesign/Cloud available but adds significant cost |
| Setup time | Minutes (sign up and run) | Days to weeks (installation, license server, configuration) |
| Learning curve | Low -- guided by conversation | High -- Maestro, command-line tools, scripting for automation |
| File format handling | Automatic conversion (PDB, SDF, MOL2, SMILES, CIF, PDBQT) | Maestro handles formats but workflows require manual prep steps |
| Structure validation | MolProbity integrated | Protein Preparation Wizard -- comprehensive, well-validated |