Pauling runs UniDock -- a GPU-accelerated fork of Vina with the same scoring function -- at 1000x throughput with automatic receptor prep, box placement, and format conversion. Zero setup. Vina itself is the most-used docking engine in academia -- free, reliable, well-cited -- but you're on your own for prep, conversion, and scaling beyond one machine.
| Category | Pauling | AutoDock Vina |
|---|---|---|
| Docking engine | UniDock -- GPU-accelerated Vina fork, same scoring function | Original Vina -- most-cited docking engine, extensively validated |
| GPU acceleration | UniDock runs on GPU -- massively parallel | CPU only; one ligand at a time per core |
| Throughput | 10M+ compounds on auto-scaling Cloud Dataflow | Hundreds to low thousands per day on a single workstation |
| Receptor preparation | Automatic -- protonation, format conversion handled by Pauling | Manual -- MGLTools/ADFR Suite for PDBQT conversion, charge assignment |
| Box placement | Automatic via P2Rank pocket detection or user-specified | Manual -- you define center and dimensions yourself |
| File format handling | Automatic conversion (PDB, SDF, MOL2, SMILES, CIF, PDBQT) | PDBQT only -- you handle every conversion |
| Scaling | Auto-scales to hundreds of workers; fault-tolerant with retries | DIY -- write your own parallelization scripts or use GNU Parallel |
| ADMET integration | Run ADMET profiling in the same workflow as docking | None -- separate tool, separate pipeline |
| Pose quality control | PoseBusters automatic QC on all docked poses | None -- manual inspection of results |
| MD follow-up | GROMACS MD with auto parameterization, MM-PBSA -- one conversation | Separate setup: GROMACS/AMBER install, topology prep, run scripts |
| Cost | Pay-per-compute on cloud infrastructure | Free and open-source |
| Scoring function | Vina scoring (via UniDock) -- same empirical function | Vina scoring -- identical, battle-tested |
| Reproducibility | Full job logging -- every parameter, input, output tracked | Depends on your own record-keeping |