Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessib...

Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.

Proteins that interact with DNA are involved in a number of fundamental biological activities such as DNA replication, transcription, and repair. A reliable identification of DNA-binding sites in DNA-binding proteins is important for functional annotation, site-directed mutagenesis, and modeling protein-DNA interactions. We apply Support Vector Machine (SVM), a supervised pattern recognition me...

Prediction of DNA-binding sites in proteins using evolutionary profiles

Recognition models to predict DNA-binding specificities of homeodomain proteins

MOTIVATION Recognition models for protein-DNA interactions, which allow the prediction of specificity for a DNA-binding domain based only on its sequence or the alteration of specificity through rational design, have long been a goal of computational biology. There has been some progress in constructing useful models, especially for C(2)H(2) zinc finger proteins, but it remains a challenging pr...

BINDING OF THE ANTITUMOR DRUG ADRIAMYCIN TO DNA-HISTONE COMPLEXES

Isotherms of the binding of the anthracycIine antibiotic, adriamycin (adriblastin), to DNA histone complexes was studied by means of spectroscopic analysis. The results indicated that: (a) binding of adriamycin to histones reduced the interaction of histones with DNA, (b) binding of the drug to DNA did not change the binding affinity of histone to DNA and, (c) in the explored binding range...