Elastic Network Model: A Coarse-Grained Approach to the Study of Biomolecular Dynamics

Over the past several decades, biomolecular dynamics has been extensively investigated through both theoretical and experimental approaches to uncover the general relationship between the native structure and biological function of proteins. In this review article, we discuss the elastic network model (ENM) and its variations, which are widely used coarse-grained approaches in biomolecular simulations. First, we summarize the pros and cons of various coarse-grained approaches, considering their computational complexity and reliability. Following that, we introduce ENM based harmonic and anharmonic analyses as tools for studying local intrinsic fluctuations and conformational transitions in proteins, respectively. We also provide a list of ENM based web servers that are open to the public. While all-atom simulations have become the gold standard in biomolecular studies today, the ENM based coarse-grained approach remains a reliable tool for long-time, large-scale protein dynamics simulations.