In summary, comparison of the mutant structure to structures of other P450s leads to the following conclusions.
The beveled angle (Figure 15) vary from structure-to-structure on same sample [80].
Secondly, the inherent buffer mechanism of the RNC isolator could successfully reduce or even prevent direct structure-to-structure pounding under severe near-fault ground motions.
The other three alignment sets (SUB177, SUB371 and HOMSTRAD) are structure-to-structure alignments used only to validate our standard soluble tables.
The quality of these alignments was assessed against the implicit sequence alignments generated by the structure-to-structure alignment program TM-align (Zhang and Skolnick, 2005).
However, they are prone to be computationally intensive due structure-to-structure comparison of all models, and are of limited use when the number of possible structures is small.
In this case the structure-to-structure alignment (by rigid-body superposition) from TM-align does not capture local similarities, leading to the 30 35% sequence identity figure, and the low assessment of performance of the other alignment methods.
Instead of a full structure-to-structure alignment, which takes O(n) time and O(n) space, pairwise base pair similarity scores are calculated using the RIBOSUM85-60 matrix for base pair substitutions (Klein and Eddy, 2003).
The alignment of each template residue in the structure-to-structure alignment produced by TM-align was compared with the alignment of the same residue produced by one of the methods.
