Protein-protein docking
The molecular docking protocol for the purpose of predicting the binding
modes and pattern of organization of each member of the CENP-HIKM
complex was conducted using ClusPro [39], which is a popularly used
tool for the docking of different proteins. ClusPro provides multiple
computational steps: rigid docking sampling of billions of
conformations, RMSD (root-mean-square deviation)-based clustering of
structures with the lowest energy (which are generated to detect the
largest clusters that will represent the complex’s closest models), and
energy minimization refinement of selected structures. ClusPro employs
PIPER, a docking algorithm that is anchored on the Fast Fourier
Transform (FFT) correlation technique, to dock the rigid body. The FFT
technique has made significant progress in rigid body protein-protein
docking [39]. The method involves placing a protein (the receptor)
at the coordinate system origin on a fixed grid and another protein (the
ligand) on a moveable grid, with the energy of interaction represented
as a correlation function. The numerical efficiency is reinforced by the
fact that such energy functions can be generated quickly, allowing for
the sampling of various conformations of protein-protein interactions as
well as the evaluation of grid point energies. As a result, a FFT-based
approach allows for protein docking without prior knowledge of their
structures [39].