Structural refinement and model quality evaluation
Following a successful modeling of each protein subunit (hs CENP-H, -I, and -K), a structural refinement protocol was conducted using the GalaxyRefine [33] which is based on a method of refinement that has successfully undergone trials in CASP10. In this method, side chains are first rebuilt and through molecular dynamics simulation, an overall structure relaxation is performed. This approach according to the assessment by CASP10 displayed the best potential in local structure quality improvement. Both local and global structure qualities were improved upon the refinement of the RaptorX Contact-generated models using this method. The quality of each refined structural model was assessed using the ProSA-web program [34] which implements the z-scoring function for structural analysis. Additional model quality assessment was conducted using the PROCHECK suite [35]. The PROCHECK suite delivers a comprehensive stereochemistry check on protein structures. The generated output is made up of several PostScript format plots and a detailed residue-by-residue listing. This highlights regions of the protein structure that might require additional investigation and also gives an evaluation of the overall structural quality in comparison to well refined structures [35].