Protein Modelling and Surface Folding by Limiting the Degrees of Freedom - Computational Modeling in Tissue Engineering - page 30

Fig. 10 Correlation between
known protein structures and
the minimized files. a The
superposition of known
(green) and minimized
(purple) models for 1CQD
globular protein from ginger
showing high match pattern
between the two structures.
b The superposition of the
known original model
(yellow) and the minimized
model (grey) for 1AQP blood
clotting protein from cattle,
illustrating the matched
regions and locations.
c Zoomed image of the
superposition at 9 Angstroms
The analysis was done using SuperPose software [ 51 ]. Minimizer output was in
the format of PDB. STRAP software was used for the PDB alignment and Clustal-W
software (Clustal-W: Multiple Alignment for DNA or Proteins, Freeware) [ 78 ] was