Using ESMFold

This tutorial shows you how to use the ESMFold model to create a PDB of your protein sequence of interest. We recommend using ESMFold with single-chain sequences. If you have a multi-chain sequence, please visit Using AlphaFold2.

What you need before getting started

Specify a sequence of interest whose structure you want to predict. The example used here is interleukin 2:

sequence = "MYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGMYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSEP"

Predicting your sequence

Call ESMFold on your sequence. The num_recycles hyperparameter allows the model to further refine structures using the previous cycle’s output as the new cycle’s input. This parameter accepts integers between 1 and 48.

Create the model object for ESMFold:

esmfoldmodel = session.fold.get_model('esmfold')
esmfoldmodel.fold?

Send the sequence of interest to ESM for folding:

esm = esmfoldmodel.fold([sequence.encode()], num_recycles=1)

esm

<openprotein.api.fold.FoldResultFuture at 0x7e063a91b5b0>

Wait for the job to complete with wait_until_done():

esm.wait_until_done(verbose=True, timeout=300)

Waiting: 100%|██████████| 100/100 [00:00<00:00, 1345.39it/s, status=SUCCESS]

True

Fetch the results with get()

The results display a tuple containing the query sequence and the contents of the resulting PDB file:

result = esm.get()
print(result[0][0])

b'MYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGMYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSEP'

Return a PDB file:

print("\n".join( list(result[0][1].decode().split("\n")[0:5]) ) )

PARENT N/A
ATOM      1  N   MET A   1       0.462 -12.684 -24.850  1.00 49.54           N
ATOM      2  CA  MET A   1       1.650 -11.836 -24.842  1.00 51.45           C
ATOM      3  C   MET A   1       1.718 -11.007 -23.563  1.00 49.89           C
ATOM      4  CB  MET A   1       1.663 -10.916 -26.063  1.00 46.31           C

Next steps

After the PDB contents are returned, save them as a file for use with your molecular visualization system of choice.