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].