Author(s): Avinash Rangaraju, Dr.A.Veerabhadra Rao
Tremendous research from last twenty years has been pursued to study various docking algorithms and predicting the active site of the molecule. Various docking programs were developed to visualize the three dimensional structure of the molecule and docking score can also be analyzed with the aid of different computational methods. Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sites and rational drug design. Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms. More importantly, experiments show that the docking quality depends on the coverage of the conformational sampling space. It is therefore desirable to accelerate the computation of the docking algorithm, not only to reduce computing time, but also to improve docking quality.