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Repeated cycles of refinement using REFMAC5 (ref. 35) and model building using COOT36 were performed.
Until now, structural analysis of the mode of binding of chemotherapeutic compounds to QR1 was based on model building using the structures of complexes with simple substrates; no structure of complexes of QR1 with chemotherapeutic prodrugs had been reported.
In phase-2, a central composite design was applied for design of experiments and model building using extraction time and extraction temperature as process variables for further maximizing the extraction of TPC.
A few cycles of refinement using Refmac5 [45] and Phenix.refine [46], interspersed with manual model building using Coot [47], were necessary to complete the model.
The structure was improved with iterative model building using COOT graphics package [33], the final structure had very good electron density (Figure 2B).
Water molecules were added using COOT, phenix.refine and by manual model building using the 2|Fo| – |Fc| and |Fo| – |Fc| maps contoured at 1σ and 3.5σ, respectively.
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Thus, also in the process of model building used within CEASAR, we dedicated the highest attention of the quality of the data used as input for our models.
Model building used O.
The cross-validated prediction error is an estimate of the prediction error associated with the algorithm for model building used.
Model building used backwards elimination method to decide on the factors to exclude from the model using the likelihood ratio test (P < 0.05).
Model building used "forced" entry to account for factors known to be associated with outcomes based on existing literature, to avoid exclusion of such factors in stepwise models.
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