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].