Comparative Study of the Prion Proteins Isolated from Reptile, Rodent, Ruminant, and Human Species using Bioinformatics Techniques

Abstract

In the present study, phylogram for each PrP sequence was generated by PAUP* 4.0 program using Neighbor-Joining method with 1,000 times bootstrapping process for the phylogenetic analysis. The molecular dynamics (MD) simulations were performed by the SANDER module in the AMBER 7 package using Amber 99 force field. All the simulation process was conducted in the IBM p690 Supercomputing System in Korea Institute of Science and Technology Information. To reduce the calculation time, we used ‘the Generalized Born (GB) model’.