A 3-d coarser-grained computational model for simulating large Protein dynamics

Protein dynamics is essential for gaining insight into biological func- tions of proteins. Although protein dynamics is well delineated by molecular model, the molecular model is computationally prohibited for simulating large pro- tein structures. In this work, we provide the three-dimensional coarser-grained anisotropic model (CGAM), which is based on model reduction applicable to large protein structures. It is shown that CGAM achieves the fast computation on low- frequency modes, quantitatively comparable to original structural model such as elastic network model (ENM). This indicates that the by model reduction method enable us to understand the functional motion of large proteins with re- markable computational efficiency.