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Topological UML modeling models structure by means of the topological class diagram.
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As with the comparisons in SURGE Next, we are finding that different structures emphasize different affordances and cognitive demands by highlighting different relationships and aspects of the models structured by the students.
The model is expanded with a wider model structure by testing formulated hypothesis about the process.
An extensive 'debudding exercise' and the review of model structure by independent clinicians were reported as internal validation [75].
To begin with, direct structure tests assess the validity of the model structure by direct comparison with knowledge about the structure of the real system.
We simplified the model structure by fixing the generally less sensitive parameter CWH at a value of 0.2, based on the suggestion by Uhlenbrook et al. ([1999]).
Crout et al. (2009) proposed a conceptually simple method for undertaking an evaluation of model structure by reducing a model through the replacement of variable quantities with constants.
It is a comparison of the PatchDock' model (this work) with the previously published model structure by Yuan et al. [PDB 3J2T] [ 25 ].
Furthermore, a transfer of the model to a location endemic for dengue may also require changes to the model structure by introducing measures for herd immunity or properties of multiple circulating dengue strains [ 34].
After performing 2,000 steps of conjugate gradient (CG) minimization, MD simulation was carried out to examine the quality of the model structure, by checking the stability via performing 2000 ps simulations at a constant temperature 300 K.
Authors' response: In the revised manuscript, we provide estimates of the changes in solvation energy of the cytochrome c upon its binding to Apaf-1 (ΔG s ) for all model structures that were obtained after energy minimization, as well as for the model structure by Yuan et al. [ 25 ]; the results are presented in the new Table 2 and discussed.
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