Protein Modelling and Surface Folding by Limiting the Degrees of Freedom - Computational Modeling in Tissue Engineering - page 32

Fig. 12 The RMSD calculations for superposition of the 1CQD with the minimized model. The
RMSD considers local and global solutions for the C a , the back bone and the heavy portion of the
atoms. The number of residues that were considered was 1,294
Fig. 13 RMSD per residue. The spikes show the difference between the original file and the
minimize file for 1CQD
folding, and also the numbers of interactions needed to give a solution, leads to the
NP problem. Furthermore, the actual environmental conditions such as interaction
of protein in an aqueous environment increase the complexity of this challenge.