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See Also
- ServiceExecute
- ServiceConnect
- BioMolecule
- BioSequence
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- Service Connections
- RCSBProteinDataBank
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See Also
- ServiceExecute
- ServiceConnect
- BioMolecule
- BioSequence
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- Service Connections
- RCSBProteinDataBank
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See Also
"ESMAtlas" (Service Connection)
Connecting & Authenticating
Requests
BioMolecule Structures
"FoldSequence" — generate 3D coordinates for a peptide sequence
"PredictedStructure" — get the predicted structure of a BioMolecule from the ESM Metagenomic Atlas database
Properties of Predicted Structures
"StructureConfidencePrediction" — get a dataset with values indicating the confidence behind the 3D embedding of the sequence.
"Sequence" — returns the BioSequence of a biomolecule from the ESM Metagenomic Atlas using the "MGnifyID"
"SequenceEmbedding" — returns the 2560-dimensional embedding vector after averaging over the final layer activations of the ESM2 model over the sequence length.
Examples
open all close allBasic Examples (1)
Create a new connection by launching an authentication dialog:
Fold a BioSequence of length 400 residues or less and obtain the predicted BioMolecule structure:
Visualize the structure of the BioMolecule :
Scope (4)
Get the predicted structure of a predicted structure from the ESM Metagenomic Atlas by providing the "MGnifyID":
Visualize the structure obtained from the database:
Get different values of prediction confidence of structures in the ESM Metagenomic Atlas:
The confidence data has the following keys:
Visualize the confidence of prediction:
Visualize the predicted alignment error, which is a measure of how confident a prediction model is in the relative position of two residues within the predicted structure. The measure is in angstroms, and the larger the value, the worse the confidence:
Get the BioSequence of a biomolecule from the ESM Metagenomic Atlas using the "MGnifyID" of the biomolecule:
Get the embedding vector after averaging over the final layer activations of the ESM2 model over the sequence length for a given protein using their "MGnifyID":
See Also
ServiceExecute ▪ ServiceConnect ▪ BioMolecule ▪ BioSequence
Service Connections: RCSBProteinDataBank
Related Links
- ▪ ESMAtlas