Indiana University-Purdue University at Indianapolis
We are interested in developing a deeper understanding of the nature of elementary processes in biological systems. Synthesizing the immense amount of molecular information generated in the current genomic era into a coherent and useful body of knowledge requires finding patterns and establishing rules to describe the behavior of the underlying molecules forming these biosystems. The application of physical principles through computer simulations of these systems allows these biomolecules to be viewed as nanomachines whose functions are related to their structures. In order to accomplish these simulations, we have employed several network-based models of protein structures. The first of these (A) is a residue-level elastic network used for simplified normal mode analysis using GNM or ANM and the second (B) is an all-atom constraint network used for rigidity analysis using FIRST.