SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.

ABSTRACT:

Motivation

Mutations that alter protein-DNA interactions may be pathogenic and cause diseases. Therefore, it is extremely important to quantify the effect of mutations on protein-DNA binding free energy to reveal the molecular origin of diseases and to assist the development of treatments. Although several methods that predict the change of protein-DNA binding affinity upon mutations in the binding protein were developed, the effect of DNA mutations was not considered yet.

Results

Here, we report a new version of SAMPDI, the SAMPDI-3D, which is a gradient boosting decision tree machine learning method to predict the change of the protein-DNA binding free energy caused by mutations in both the binding protein and the bases of the corresponding DNA. The method is shown to achi

SUBMITTER: Li G 

PROVIDER: S-EPMC10186157 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature