In this work, we have developed an optimization framework for digging out common structural patterns inherent in DNA binding proteins. A novel variant of the artificial bee colony optimization algorithm is proposed to improve the exploitation process. Experiments on four benchmark objective functions for different dimensions proved the speedier convergence of the algorithm. Also, it has generated optimum features of Helix Turn Helix structural pattern based on the objective function defined with occurrence count on secondary structure. The proposed algorithm outperformed the compared methods in convergence speed and the quality of generated motif features. The motif locations obtained using the derived common pattern are compared with the results of two other motif detection tools. 92% of tested proteins have produced matching locations with the results of the compared methods. The performance of the approach was analyzed with various measures and observed higher sensitivity, specificity and area under the curve values. A novel strategy for druggability finding by docking studies, targeting the motif locations is also discussed.
Keywords: Optimization approach; artificial bee colony algorithm; employee bees; helix turn helix motif; neighbor selection; optimum pattern.