A linear scale to estimate DNA-binding free energy of amino acid residues is reported. Scales derived exclusively for irregular and helical positions give 76% and 68% classification accuracy between stabilizing and destabilizing protein-DNA interaction. Mean absolute error (MAE) in ddG values is 0.786 and 0.883 kcal/mol respectively. Without using structure information of residues to derive affinity scales, 67.0% mutations could be correctly classified between those stabilizing and destabilizing binding. Mean absolute error (MAE) and correlation of ddG predictions are 0.953 kcal/mol and 0.385 respectively. PRIB 2008 proceedings found at: http://dx.doi.org/10.1007/978-3-540-88436-1 Contributors: Monash University. Faculty of Information Technology. Gippsland School of Information Technology ; Chetty, Madhu ; Ahmad, Shandar ; Ngom, Alioune ; Teng, Shyh Wei ; Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB) (3rd : 2008 : Melbourne, Australia) ; Coverage: Rights: Copyright by Third IAPR International Conference on Pattern Recognition in Bioinformatics. All rights reserved.