Abstract

The high accessibility of genomic data and expression data has opened the possibilities for the target protein analysis. The full information about the protein structure affords well-founded hypothesis of the function of protein. Once the structure of the protein binding site is known, the applications of the drug discovery methods are done. The steric and complementarity of binding site of protein and drug molecule provides the complete information for structural design. We have employed protein threading and homology based prediction for the structure of DNA topoisomerase II from Escherichia coli. DNA topoisomerases catalyze topological interconversions: supercoiling relaxation, catenation decatenation and knotting unknotting of DNA, consist of GyrA and GryB subunit. In this paper we have described the docking for structure based drug design. Protein function can be predicted in number of ways from the sequence. Since the function of protein is based on protein domains, a number of databases like Pfam, PROSITE, PRINTS, ProDom, SwissPROT + TREMBL are used. Protein folds are evaluated by SCOP and CATH. The structural accepts predicted by the computational methods are expected to invade the search of target proteins and the development of new drugs.