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Although FeSII and Gdia0615 models were built from different template structures, they share many structural features.
Root mean square differences ranging from 0.88 to 3.26 Å indicate structural conservation between the target and template structures.
A structural model of Ycf39 was built using template structures found on HHpred server [ 69].
This program uses variable gap penalty for structural loops and core regions using information derived from template structures.
Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each.
Depending on the template structures, the carbon patterns can be quadrangular or hexagonal in shape.
The sequences of Rat1∆NLS and Xrn1 were aligned with the sequences of template structures of S. pombe and K. lactis taken from the Protein Data Bank (PDB 54, with codes 3FQD and 3PIF, respectively.
Figure 5 Representative examples of template structures for glycerophospholipids (GP).
Figure 7 Representative examples of template structures for sphingolipids (SP).
The standard template structures included in FlaME are: cyclopropane, cyclobutane, cyclopentane, cyclohexane, benzene, cycloheptane, and cyclooctane.
The loop/junction structures are built from the virtual bond fragments of the template structures.
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