Welcome to Gpolate
Prediction of DNA-binding Free Energy Change (ddG) upon mutation

This server predicts change in DNA-binding free energy in proposed mutations in a protein using information about
1. The identity of mutated and mutant residues,
2. Thermodynamic information of pH and Temperature and
3. Structure information of protein in the form of Secondary Structure and Solvent accessibility.





Please select mutated residue (name of the residue to be replaced).
Please select mutant residue (name of the new residue).
Enter pH value.
Enter Temperature (in Celsius)
Choose the secondary structure of mutated residue.
Enter the value of solvent accessibility (ASA) of the mutated residue in its un-complexed form (absolute area units).
NOTES:
Current web server is expected to provide predictions of ddG with following performance scores
Mean absolute error in ddG: 0.945 kcal/mol
Correlation between predicted and experimental values: 0.416
Average classification accuracy (number of correctly classified mutation/ number of mutations): 70.3%
Sensitivity for classification between stabilizing and destabilizing mutations: 84.9%
Specificity for classification between stabilizing and destabilizing mutations: 47.9%
Average of sensitivity and specificity: 66.4%
Following options are currently not implemented because of few training data available at the moment.
It is hoped that future versions will improve performance of this server by including following features.
These will be included in when enough training data becomes available.
1. N-terminal neighbor of mutated residue.
2. C-terminal neighbor of mutated residue.
3. Information of DNA.


For questions or commemts, please contact Shandar Ahmad: shandar@sciwhylab.org.