The AI Folding API provides a common interface to AI based protein structure prediction tools. The API currently supports OpenFold, AlphaFold, and ESMFold. The API runs a post-processing protocol on the results to minimize the output structure into the Rosetta energy function and correct any atomic level errors in sidechain positioning (See Notes for more detail).

Contents

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• --ai-toolAI folding tool to run (openfold, alphafold, esmfold), default = alphafold

• --mode Mode to run with AI tool (monomer, multimer, singleseq), default = monomer

• --model-sets The set of model weights to use with OpenFold (alphafold, openfold), default = openfold (See Notes for more detail)

• --existing-model-data Location of existing model data in GCS, default = null

• --precomputed-alignments Directory path to precomputed alignments that will be upload and used for AlphaFold jobs, default = null

• --run-relax Enable or disable the Rosetta relax phase of post-processing, default = true

• --gpu-type Select the GPU type to use (t4, a100), default = t4 (See Notes for more detail)

Outputs

• predictions (directory) AI tool model predictions

• initial_molprobity_reports (directory) Molprobity report for models output by AI tool

• rosetta_relaxed_models (directory) Rosetta relaxed AI tool models

• final_molprobity_reports (directory) Molprobity report for relaxed models

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References

AlphaFold Github

OpenFold Github

ESMFold Github