A graph kernel method for DNA-binding site prediction.

ABSTRACT:

Background

Protein-DNA interactions play important roles in many biological processes. Computational methods that can accurately predict DNA-binding sites on proteins will greatly expedite research on problems involving protein-DNA interactions.

Results

This paper presents a method for predicting DNA-binding sites on protein structures. The method represents protein surface patches using labeled graphs and uses a graph kernel method to calculate the similarities between graphs. A new surface patch is predicted to be interface or non-interface patch based on its similarities to known DNA-binding patches and non-DNA-binding patches. The proposed method achieved high accuracy when tested on a representative set of 146 protein-DNA complexes using leave-one-out cross-validation.

SUBMITTER: Yan C 

PROVIDER: S-EPMC4290685 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature