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%.