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Instant-use add-on functions for the Wolfram Language
As of Version 14.1, use the BioMoleculePlot3D built-in symbol.

Function Repository Resource:

 ESMFoldProteinSequence

Source Notebook

Fold a protein using the ESMFold API

Contributed by: Jan Mangaldan

ResourceFunction["ESMFoldProteinSequence"][p]

shows a visualization of the protein structure represented by the sequence p predicted using the ESMFold API.

Details

p can be a string of one-letter amino acid abbreviations, or a BioSequence of "Peptide" type. The documentation for BioSequence gives the list of amino acids corresponding to each letter.
The ESMFold API is currently limited to sequence lengths of up to 400.
p can also be a "Protein" entity.
ESMFoldProteinSequence takes the same options as Graphics3D.

Examples

Basic Examples (1) 

Visualize the structure of a protein sequence as predicted by ESMFold:

In[1]:=
ResourceFunction[ "ESMFoldProteinSequence"]["TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN"]
Out[1]=

Scope (2) 

Visualize the folding of a peptide represented as a BioSequence:

In[2]:=
ResourceFunction["ESMFoldProteinSequence"][ BioSequence[ "Peptide", "GSGHMDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRILYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNRE", {}]]
Out[2]=

Predict the structure of a protein Entity:

In[3]:=
ResourceFunction["ESMFoldProteinSequence"][Entity["Protein", "NEDD8"]]
Out[3]=

Compare with the known structure:

In[4]:=
EntityValue[Entity["Protein", "NEDD8"], EntityProperty["Protein", "StructureDiagram"]]
Out[4]=

Version History

  • 1.0.0 – 25 May 2023

Source Metadata

  • Citation:
    • Lin Z. et al., "Evolutionary-scale prediction of atomic-level protein structure with a language model." Science, vol. 379, no. 6637, 1123-1130, 2023.
      DOI: 10.1126/science.ade2574

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