Pauling is the pipeline -- 15+ validated tools integrated end-to-end, accessible through conversation, maintained by us. Building in-house means six months stitching together AutoDock, GROMACS, RDKit, OpenBabel, and a dozen Python scripts. Then maintaining it forever.
| Category | Pauling | In-House Pipeline |
|---|---|---|
| Development time | None -- ready to use immediately | 6--12+ months to build, debug, and validate |
| Tools integrated | UniDock, GROMACS, P2Rank, MolProbity, PoseBusters, ADMET profiling -- pre-wired | You integrate each tool manually (AutoDock, GROMACS, RDKit, OpenBabel, etc.) |
| Maintenance burden | Zero -- Pauling team handles updates | Every dependency update can break your glue code |
| File format handling | Automatic conversion across PDB, PDBQT, SDF, MOL2, CIF, SMILES | You write and maintain format converters (OpenBabel wrappers, custom parsers) |
| Scaling | Auto-scales to 10M+ compounds on Cloud Dataflow | Limited by your hardware; parallelism is hand-rolled |
| Quality control | Built-in: PoseBusters pose QC, MolProbity structure validation | You implement your own QC checks -- or skip them |
| Reproducibility | Full job tracking -- every parameter, input, output logged | Depends on your discipline with version control and logging |
| Team expertise required | Conversational interface -- any bench chemist can run jobs | Requires Python/Bash scripting + sysadmin + comp chem expertise |
| Ligand parameterization | Automatic via ACPYPE for MD | Manual ACPYPE/GAFF setup per ligand |
| Binding energy validation | MM-PBSA integrated into MD workflow | You set up gmx_MMPBSA or write your own scripts |
| Cost | Pay for compute usage | Developer salaries + compute + ongoing maintenance time |
| Customization | Covers standard CADD workflows end-to-end | Full control -- build exactly what you need |