Date of Award


Publication Type

Master Thesis

Degree Name



Computer Science

First Advisor

Mukhopadhyay, Asish


Center star method, Dynamic programming, Multiple protein structure alignment




There is a buzz among structural biologists about conducting a major portion of their future work in silico, due to progressively refined computational tools and an amazing quantity of digitized biological data. This masters thesis focusses on the area of computational methods for aligning multiple protein structures. As the problem under consideration is known to be np–complete, several ways for coming up with good approximations have been suggested over the years. A new approach for achieving better, or at least as good results as before, is presented here. We discuss the proposed algorithm and its constituent methods. Finally, we report the widely used root mean square deviation (RMSD) as measures of structural similarity, and the execution time. Some chosen results, from our extensive experimentation, and their significance have been discussed. A web server has also been implemented for trying out a pairwise alignment algorithm. This is hosted on the university website and the link has been provided in the contributions