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This documentation is deprecated, please use the new documentation site instead.

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


  • 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. 


Output file descriptions

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

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%.