SAMPDI-3D: Predicting protein-DNA binding free energy change upon mutations

Emil Alexov Group


A user can download a sample protein-DNA complex structure 1AAY.pdb and a protein-mutation-list-file and/or a DNA-mutation-list-file for executing the example. Note to carry out a protein/DNA mutation effect prediction in single mode, one can try a single mutation row information and feed in the single mode form.

SAMPDI-3D predicts the effect of mutation of protein or DNA on protein-DNA binding. The mutation can be in (1). protein or in (2). DNA, each of the two cases has two different modes: Single mode, and multiple mode, both are exemplified below.

User Input for Protein Mutations (1) as shown in Figure 1.

form-filled Figure 1. Example for protein mutation input form.

User Input for DNA Mutations (2).


Figure 2. Example for DNA mutation input form.



Figure 3. SAMPSI-3D results for example for protein/DNA mutation.

Copyright © Computational Biophysics and Bioinformatics - Emil Alexov Group.