Biomedical Engineering Reference
In-Depth Information
Fig. 9 The RMSD per residue, with the spikes showing the difference between the original file
and the minimized file for 1AQ5
1AQP, a blood clotting protein from Bos Taurus (cattle), has been modeled in
1997 via X-ray diffraction [ 6 ]. Figure 10 b shows the superposition of the known
model and the minimized model. The grey color shows the superimposed model
matching the original file. Figure 10 c shows ribbons to depict the protein and the
minor differences between the original file in yellow and the minimized file in
gray; the distances of the differences are at *9 Å. Figure 14 shows the local and
global RMSD of the a-carbon and Back Bone. The local gives the RMSD per
amino acid per carbon bone and the global gives the RMSD of the sequence of 124
residues.
To further validate our methods, we compared the predicted structures with the
respective PDB entries using the alignment program STRAP [ 29 , 33 , 34 ] freely
obtainable from http://3d-alignment.eu/ . To compare two given 3D-structures of
proteins, STRAP uses the method of 3D-superposition. STRAP implements sev-
eral different back-ends for computation. Here TM-align [ 88 ] was used to perform
a rigid superposition. TM-align moves one of the two models in space until both
structures coincide as best as possible. There is a trade off between a low RMSD
and a high percentage of assigned C-alpha positions. The result is a translation
vector and rotation matrix. STRAP processes the result. It determines the RMSD
which is a measure for the dissimilarity of two structures, derives a (multiple)
sequence alignment and visualizes the result in Pymol [ 25 ].
Search WWH ::




Custom Search