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cyrus submit ai-folding input.fasta --mode=monomer --ai-tool=openfold
To submit an alphafold SingleSeq job you can set the mode to “singleseq” and specify the number of recycles with the “af-n-recycles” flag:
cyrus engine submit ai-folding input.fasta --mode singleseq --ai-tool alphafold --af-n-recycles 2
Multiple fasta files can be evaluated in a single job like this:
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The AI Folding API runs a post-processing protocol on the results of the AI tool. The purpose of the post-processing is to minimize the output structure into the rosetta energy function and correct any atomic detail level errors in sidechain positioning. The protocol consists of the following three steps
Generate a molprobity report for the models output from the AI tool
Idealize and relax the models output from the AI tool with rosetta
Generate a molprobity report for the rosetta relaxed models.
Alongside the raw output from the AI tool, the API will produce the following directories:
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