The dynamics of protein structures play an important role in cell life and their biological functions involves molecular motion within the cell to adapt and evolve new functions. Therefore, a full understanding of protein function will require deeper insight into biomolecular dynamics. Molecular dynamics simulations are powerful tools that are available to explore the dynamics of protein conformations, which are often a critical element of their function. Studying and exploring the functionally relevant conformations are done by clustering large ensemble of proteins structures that are generated by molecular simulation. The recently completed wheat genome project and transcriptome analysis has helped in identifying various genes / proteins that are important towards abiotic stress. In this proposal, we aim to study structural dynamics of different proteins of the wheat genome, which play an important role towards salt stress, using molecular simulation. The RNAseq data is a resource to find genes with significant expression differences under salt stress . Then we will compare those patterns in two mutagenized lines and search for SNPs in genes with large variations to see if they can be treated as potential genetic markers for breeding purposes.