Normal mode analysis and changes in vibrational entropy
The normal mode dynamics of the hypothetical hs CENP-HIKM complex was assessed using the iMOD [40] and DynaMut [41] tools. This analysis was directed at determining the stability of the docked complex and also for the exploration of the protein-protein interaction dynamics. iMOD analyses conformational flexibility of nucleic acid and protein structures by utilizing the normal mode analysis in internal coordinates. Considering the dihedral angles as variables, lowers the non-physical distortions and cost of computation of classical Cartesian normal mode analysis approaches. Operation of the framework is at various coarse-grained levels and delivers an active framework for the conduction of normal mode analysis-based conformational studies which include pathway exploration, vibrational analysis or Monte-Carlo simulations [40]. The iMOD normal mode analysis also function as a rational option for atomistic simulation. The stiffness of motion is presented by a given value while covariance matrix, eigenvalue, deformability and elastic network model are also calculated [40]. DynaMut on the other hand implements normal mode analysis using two different methods, ENCoM and Bio3D, delivering simplified and rapid access to insightful and efficient protein motion analysis [41]