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]