The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules
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Structural biology techniques, such as nuclear magnetic resonance (NMR), x-ray crystallography, and cryogenic electron microscopy (cryo-EM), have provided extraordinary insights into the details of the functional configurations of biomolecular systems. Recent advances in x-ray crystallography and cryo-EM have allowed for structural characterization of large molecular machines such as the ribosome, proteasome, and spliceosome. This deluge of structural data has been complemented by experimental techniques capable of probing dynamic information, such as Förster resonance energy transfer (FRET) and stopped flow spectrometry. While these experimental studies have provided tremendous insights into the dynamics of biomolecular systems, it is often difficult to combine the low resolution dynamical data with the high-resolution structural data into a consistent picture. Computer simulation of these biomolecular systems bridges static structural data with dynamic experiments at atomic resolution (Fig. 1).