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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 please contact the engineering team before starting as the project will likely require a larger than normal GPUadd 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 ai-folding input.fasta --mode=monomer --ai-tool=openfold --model-sets=alphafold
When modeling a large protein, you can use a larger a100 GPU with --gpu-type=a100 and disable the rosetta relax post-processing step with --run-relax=false
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Currently, openfold does not support multichain modeling |
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