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%.