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

Quickstart

Command Line Examples

Submit a PDB for solubility scoring:

cyrus engine 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")

Inputs

• --pdb-file

  • Input PDB file — cleaned and/or relaxed PDB

  • Prepare a clean PDB using the Clean PDB API

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

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

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

  • Cyrus strongly recommends using the Relax API on your PDB prior to using this API.

Outputs

• predictions.csv

  • CSV file containing solubility prediction information, containing:

    • Total solubility score for the structure

    • per-residue solubility scores

    • per-residue SASA percentages

    • per-residue absolute SASA in angstroms (Å)

Notes

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%.