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Quickstart

Model a monomer using AlphaFold

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

Model multiple monomers in parallel using OpenFold

cyrus engine submit ai-folding input.fasta input2.fasta --mode=monomer --ai-tool=openfold

Model a monomer using OpenFold with weights trained by DeepMind (AlphaFold)

Default = OpenFold weights

cyrus engine submit ai-folding input.fasta --mode=monomer --ai-tool=openfold --model-sets=alphafold

Create a model using AlphaFold's SingleSeq mode with 2 recycles

cyrus engine submit ai-folding input.fasta --mode=singleseq --ai-tool=alphafold --af-n-recycles=2

Model a multimer (AlphaFold only)

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

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FASTA file containing sequence(s) of interest to model.

Options

• --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), 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

Notes

Model weight sets

• alphafold - weights trained by DeepMind

• openfold - weights trained by the AlQuarashi Lab for OpenFold

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