Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions.

ABSTRACT: Protein-DNA interactions are crucial to many cellular activities such as expression-control and DNA-repair. These interactions between amino acids and nucleotides are highly specific and any aberrance at the binding site can render the interaction completely incompetent. In this study, we have three aims focusing on DNA-binding residues on the protein surface: to develop an automated approach for fast and reliable recognition of DNA-binding sites; to improve the prediction by distance-dependent refinement; use these predictions to identify DNA-binding proteins. We use a support vector machines (SVM)-based approach to harness the features of the DNA-binding residues to distinguish them from non-binding residues. Features used for distinction include the residue's identity, charge, solvent a

SUBMITTER: Bhardwaj N 

PROVIDER: S-EPMC1993824 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature