Challenges and Opportunities for the Visualization of Protein Energy Landscapes

Protein folding is the process by which proteins go from a linear chain of amino acids to a 3-D structure that determines their biological function. Although recent advances in protein 3-D structure prediction can directly determine the folded protein's final shape, the process by which this happens is complex and not very well understood. Part of the study of protein folding focuses on the analysis of their "energy landscape," defined by the molecule's energy as a function of its structure. The data are mostly obtained through atomic-level computer simulations and are very high-dimensional, making them difficult to interpret. Visualization can be a powerful tool to support researchers studying the energy landscape of proteins; however, we noticed that they are not widely adopted by the scientific community. We present the main methods currently used and the challenges they face, as well as future opportunities for visualization in this field.