DNA-binding proteins play an important role in most cellular processes, such as gene regulation, recombination,
repair, replication, and DNA modification. In this article, an optimal Chou’s pseudo amino acid composition
(PseAAC) based on physicochemical characters of amino acid is proposed to represent proteins for identifying DNAbinding
proteins. Six physicochemical characters of amino acids are utilized to generate the sequence features via the web
server PseAAC. The optimal values of two important parameters (correlation factor λ and weighting factor w) about
PseAAC are determined to get the appropriate representation of proteins, which ultimately result in better prediction performance.
Experimental results on the benchmark datasets using random forest show that our method is really promising
to predict DNA-binding proteins and may at least be a useful supplement tool to existing methods.