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 please contact the engineering team before starting as the project will likely require a larger than normal GPU
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 ).
To model a single chain protein with alphafold or openfold
cyrus submit ai-folding input.fasta --mode=monomer --ai-tool=alphafold
cyrus submit ai-folding input.fasta --mode=monomer --ai-tool=openfold
Currently, openfold does not support multichain modeling
To model a prokaryotic multichain protein with alphafold
cyrus submit input.fasta --mode=multimer --ai-tool=alphafold --is-prokaryote true
To model a eukarytotic multichain protein with alphafold
cyrus submit input.fasta --mode=multimer --ai-tool=alphafold --is-prokaryote false
The workflow produces a single output artifact containing the results of modeling. An explanation of the output files can be found here: https://github.com/deepmind/alphafold#alphafold-output