Protein Modelling and Surface Folding by Limiting the Degrees of Freedom - Computational Modeling in Tissue Engineering - page 26

Fig. 4 Correlation between
known protein structures and
the minimized files.
a Superposition of 1BBF
collagen protein shown by the
green is the known original
and the blue-green line is
minimized file showing
excellent fit between the two
models. b The frontal view of
the superimposed files of
original (pink) and the
minimized (purple) models
(with side chains) for 1AQ5
chicken cartilage matrix
protein. Near-identical
structural correlation was
seen. c Side view of the
superposition; of note are the
tips of the coils that show the
same alignment
superposition of the known and the modeled protein. The heavy atoms (one with a
significantly higher atomic scattering factor than the others) are derivative struc-
ture factor amplitudes or changes along RMSD per molecule. The non-bonding
energies used in order to minimize modelling of inter-molecular interactions can
be integrated to the trilateration model [ 40 ].