Pauling runs real pipelines -- docking, MD, ADMET, binding-energy calculation -- real physics, real results you can take to the lab. Gemini Deep Research is excellent at literature synthesis and scientific reasoning, but it does not dock molecules, run molecular dynamics, or calculate binding energies.
| Category | Pauling | Gemini Deep Research |
|---|---|---|
| Molecular docking | UniDock (GPU-accelerated Vina) with ranked poses and scores | Cannot execute docking calculations |
| Molecular dynamics | Full GROMACS MD with checkpoint save/resume, ACPYPE ligand parameterization | Cannot run MD simulations |
| ADMET prediction | Integrated ADMET profiling pipeline | Can discuss ADMET properties conceptually, no computation |
| Virtual screening | 10M+ compounds via Cloud Dataflow auto-scaling | Cannot screen compound libraries |
| Structure validation | PoseBusters pose QC + MolProbity structure checks | No structural validation tools |
| Binding energy calculation | MM-PBSA from explicit MD trajectories | Cannot compute binding free energies |
| Scientific reasoning | Guided by quantitative simulation outputs | Excellent -- multi-step reasoning across large literature corpora |
| Multimodal analysis | Focused on molecular structures and numerical data | Strong -- can analyze figures, charts, protein images from papers |
| Actual computation | Every output from real physics-based pipelines on cloud GPUs | Zero -- text generation only, no molecular software |
| File format handling | Automatic PDB, PDBQT, SDF, MOL2, CIF, SMILES conversion | Cannot parse or manipulate molecular file formats |
| Reproducibility | Full parameter logging, jobs dashboard, trajectory files | Responses vary per session -- no deterministic computation |