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. 

Outputs

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%.