TY - EJOU AU - Kim, Jae-In AU - Jang, Hyoseon AU - Ahn, Jeong-Hee AU - Eom, Kilho AU - Na, Sungsoo TI - A 3-D Coarser-Grained Computational Model for Simulating Large Protein Dynamics T2 - Computers, Materials \& Continua PY - 2009 VL - 9 IS - 2 SN - 1546-2226 AB - Protein dynamics is essential for gaining insight into biological functions of proteins. Although protein dynamics is well delineated by molecular model, the molecular model is computationally prohibited for simulating large protein 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 CGAM by model reduction method enable us to understand the functional motion of large proteins with remarkable computational efficiency. KW - Protein Dynamics KW - Elastic Network Model KW - Coarser-Grained Anisotropic Model KW - Low-Frequency Mode DO - 10.3970/cmc.2009.009.137