Solubility Scoring

Owned by Sam DeLuca, created
Last updated: Nov 09, 2023 by Aaron Aguhob
1 min read

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%.