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The amount of GPU memory required by alphafold and openfold increases quadratically with the number of amino acids in the system being modeled. If you are modeling a protein complex longer than 1500 residues or so add the following options to the ai-folding submit command: --gpu-type=a100 --run-relax=false |
Using the API
The “AI Folding” api provides a common interface to AI based protein structure prediction tools. The API currently supports openfold (https://github.com/CyrusBiotechnology/openfold) and alphafold ( https://github.com/deepmind/alphafold#alphafold-output ).
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cyrus submit input.fasta --mode=multimer --ai-tool=alphafold
API Outputs
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
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