Common interface to protein design tools and structure predictors
This package provides three things:
- A huge docker image with a number of protein design and protein structure prediction tools installed (with model weights) in the same python environment
- A python API to call (most of) these tools using a reasonably convenient interface
- A flask server with an API to call these tools over HTTP
This is all very much WIP. Contributions are welcome.
| Tool | Task | Installed in the proteopt docker image? | Part of proteopt python API? | Unit tests for API |
|---|---|---|---|---|
| AlphaFold | structure prediction | yes | yes | yes |
| OmegaFold | structure prediction | yes | yes | yes |
| OpenFold | structure prediction | yes | no | no |
| ESMFold | structure prediction | no (TODO) | no | no |
| RFDesign hallucination | design | yes | yes | yes |
| RFDesign inpainting | design | yes | yes | yes |
| ProteinMPNN | fixed-backbone design | yes | yes | yes |
| ColabDesign AfDesign | design | yes | no | no |
| RFDiffusion | design | yes | yes (motif scaffolding only) | yes |