Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group

SAMPDI Web Server

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: Link

Bioinformatics. 2018 Mar 1;34(5):779-786. doi: 10.1093/bioinformatics/btx698.

Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.

Peng Y , Sun L , Jia Z , Li L , Alexov E .

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

Click on the following links to obtain a sample PDB file along with instructions of selecting parameter and predicted results.

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