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In the development of a computational model for prediction of structural specificity of substrate compounds to BCRP, three dimensional structures of the substrates were built using AMPAC with Graphical User Interface (Semichem, Shawnee Mission, KS).
The structures of the substrates used in the study are shown.
The structures of the substrates in the training set are shown in Figure 5.
The structures of the substrates were shown (Fig. 7). Figure 7 Chemical structure of saccharides.
Three dimensional structures of the substrates were built using AMPAC with Graphical User Interface (Semichem, Shawnee Mission, KS) [56].
In our approach, we use only the structures of the substrates for the prediction of the reacting atoms.
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The structures of the substrate binding sites in the different states are described producing a full picture of the translocation events in the AAC.
We use only the known information of the structures of the substrate and metabolite of the reactions for the creation of training sets to predict the reacting atoms of nine classes of reactions.
The catalytic amino acid residues are known and are identical between the two enzymes although the exact structures of the substrate binding pockets remain to be determined.
As shown in the examples reported here, the molecular cavity itself can be involved as a recognition unit for inclusion of the substrate or of part structures of the substrate.
The structures of the substrate complex in three different crystals (anion-free, fluoride-soaked, and azide-soaked) are compared.
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