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).

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cyrus engine submit ai-folding input.fasta --mode=monomer --ai-tool=alphafold```alphafold

Model multiple monomers in parallel using OpenFold

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• --ai-tool

  • AI 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) (See Notes for more detail)

  • default = openfold

• --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 false

• --gpu-type

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

  • default = t4

Outputs

• alignments (directory)

  • Alignment data relevant to AI tool predictions

• 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