Protein Structure Quality Score (PSQS)
PSQS is an energy-like measure of the quality of
protein structure. It is calculated based on the statistical potentials of mean
force describing interactions between residue pairs and between single
residues and solvent. Three sets of statistical potentials have been obtained
from the statistics calculated for representative set of 1836 proteins containing
all domain folds available in the SCOP database:
- Local potential - describes local geometry propensities of polypeptide
chain. It is a function of residue types of residues i-1, i and i+1.
- Burial potential - describes the tendency of hydrophobic residues
to concentrate in the protein core and the tendency of hydrophilic residues
to concentrate on the protein surface.
- Contact potential - describes the likelihood of different residue
pairs to be in close contact.
The program calculating PSQS was developed at
Godzik Lab, Burnham Institute.
To calculate PSQS for your protein submit the structure file in PDB format.
You may also submit series of structures from refinement to see all psqs graphs together.