SAMPDI: The effect of single amino acid substitution on the binding free energy of protein-DNA complex
Professor Emil Alexov Group
About SAMPDI
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.
Peng, Y.; Sun, L.; Jia, Z.; Li, L.; Alexov, E. Predicting protein–DNA binding free energy change upon missense mutations using modifie d MM/PBSA approach: SAMPDI webserver. Bioinformatics 2018, 34(5), 779–786. https://doi.org/10.1093/bioinformatics/btx698