proteopt

Common interface to protein design tools and structure predictors

This package provides three things:

1. A huge docker image with a number of protein design and protein structure prediction tools installed (with model weights) in the same python environment
2. A python API to call (most of) these tools using a reasonably convenient interface
3. A flask server with an API to call these tools over HTTP

This is all very much WIP. Contributions are welcome.

Tools

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