Protein–DNA interactions are essential for many important cellular processes and mutations occurring
in DNA-binding protein have profound effect on protein-DNA interactions and are linked with many
diseases. SAMPDI Web Server provides fast and accurate predictions for the effects of single amino
acid substitution on the binding free energy of protein-DNA complex. This method utilizes modified
molecular mechanics Poisson-Boltzmann Surface Area (MM/PBSA) approach along with an additional set
of knowledge-based terms delivered from investigation of the physico-chemical properties of
protein-DNA complexes. Important feature is applying DelPhi Gaussian-based smooth dielectric
function to calculate the change of solvation energy.
If the usage of the server results in scientific publication, please, cite the following papers:
2017 Oct 28. doi: 10.1093/bioinformatics/btx698. [Epub ahead of print]
Predicting protein-DNA binding free energy change upon missense mutations using modified
MM/PBSA approach: SAMPDI webserver.
SAMPDI is running on Clemson University's Palmetto Supercomputer Cluster.
If you experience problems, they may be due to Palmetto Cluster being not functional or under
maintenance. Contact us at firstname.lastname@example.org.