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This framework demonstrates that post-design analysis supports the discovery of missing requirements and can guide the model refinement cycle.
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REFMAC5 [43] was used for refinement of the data and after each refinement cycle model building was performed in COOT.
Manual model rebuilding between refinement cycles was performed using Coot [40].
DOI: http://dx.doi.org/10.7554/eLife.01299.013 10.7554/eLiFigure99.014 figure 4—figure supplement 3. Incorrect MCP model obtained by enforcing the HK97 topology into the BPP-1 MCP cryoEM density, followed by five cycles of model refinement ('interchanged model').
For the thermolysin structure obtained from anomalous diffraction data (processed keeping Friedel pairs separate), only one cycle of atomic model refinement was carried out.
Alternating model-building and refinement cycles using REFMAC5 [ 25] were performed with appropriate entries made in the dictionary for AcCoA.
This model comparison focusses on the notion of model refinement that often occurs in the life-cycle of published biological models.
A continual cycle of modeling, hypothesis generation, experimentation, and model refinement is proposed as the only logical way for biology to move forward.
An iterative cycle of model predications, experimental validation, and model refinement will therefore lead to an improved quantitative understanding of the interactive mechanisms underlying amino acid transfer as a biologic system in both health and disease.
Figure 2 The service refinement cycle.
We then enter the iterative refinement cycle.
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