Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group

SAMPDI Web Server

Protein–DNA interactions are essential for the regulations of many important cellular processes and single mutations occurring in DNA-binding protein have profound effect on protein-DNA interactions and are related 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 and results in good agreement with experimental data.

If the usage of the server results in scientific publication, please, cite the following papers: Link

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

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