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).

...

Quickstart

Command Line Examples

Submit a PDB for solubility scoring:

cyrus engine submit solubility-score input.pdb

...

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:

  the total

  • • 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 (Å)

Notes

Output File interpretation

...