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There are number of parameters need to be set before building the initial model.
In building the initial model of LY30 effects, we interpolated from a few measured time points of cFLIP, to obtain a simple approximation of LY30-induced decay of cFLIP, using a constant degradation rate (Supplementary Material 1.4).
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The iterative steps we followed in building the initial PT are summarised in table 2 below.
Numerous metabolic and physicochemical aspects about AS had to be considered in the initial model building.
This model was built using a novel scheme for model reconstruction based on high throughput proteomic data at the initial model building phase.
The initial model building study set consisted of 5022 Caucasian females: 1671 breast cancer cases and 3351 age-matched cancer-free controls, and the validation study set consisted of 1193 Caucasian females: 400 breast cancer cases and 793 age-matched cancer-free controls.
Automated model building in ARP/wARP was utilized to generate the initial model.
The initial model used for building was that of the WT MauG preMADH complex [Protein Data Bank (PDB) entry 3L4M] with solvent and ligands removed, and Gln103 mutated to Asn.
Refmac5 and PHENIX.REFINE, together with intermittent manual building in COOT were used to correct and improve the initial model produced by PHASER.
The initial model was improved by visual inspection and model building with COOT [52].
Comparing the whole-building energy modeling results with the overall measured energy consumption, the building shows approximately 60% higher energy consumption during its first year of operation than the initial model prediction.
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