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The solubility scoring API predicts the solubility of an input protein structure.

Inputs

  • Input PDB file — a PDB file with the residues starting at 1 and increasing monotonically (1,2,3,4,…).  Files downloaded from Cyrus Bench will be formatted in this way.  

    • CLI argument: --pdb-file input.pdb

    • Python submit() argument: pdb-file=”input.pdb”

    • Do not include nonprotein residues.

    • Do not include multimodel (NMR-sourced) PDBs.  

    • This numbering requirement is relaxed if you do not use residue sets (below).

    • Cyrus strongly recommends using the Prepare or Relax tool in Cyrus Bench to preprocess models before uploading to this API. 

Command Line Examples

Submit a PDB for solubility scoring:

cyrus submit solubility-score input.pdb

Python Examples

Submit a PDB for solubility scoring:

from engine.solubility_score.client import SolubilityScoreClient

client = SolubilityScoreClient()
job_id = client.submit(input_pdb="input.pdb")

Outputs

This API returns a CSV file containing solubility prediction information. It contains:

  • the total solubility score for the structure

  • a list of per-residue solubility scores

  • a list of per-residue SASA percentages

  • a list of per-residue absolute SASA in angstroms

Output File interpretation

The solubility score is a measure of how aggregation-prone a residue or structure is, with higher scores representing higher aggregation propensity. The SASA percentage is the accessible surface area when compared to the same residue in a GLY-X-GLY peptide (1.00 meaning 100%, or as exposed as the very-exposed same residue in the GLY-X-GLY peptide). This value may be slightly over 100%.

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