Docking Modelling Receptor

Virtual library A combinatorial library that has no physical existence rather, it exists in a computer or on pjiper. Such libraries cun be generated automatically and. screened against physiocheniicul filters like the "rule of five" or be docked into receptors by use of molcx ular modeling. 

The orientation of type IV for salvinorin A in our model differs from the docking models reported by Roth and colleagues [32, 33] and by Kane et al. [34, 35] (Fig. 14). In our model, salvinorin A avoided the position of the charged NH+ group (HD1), that is, the vicinity of the conserved Aspl38 in all opioid receptors,... 

Table VIII below shows five examples of the homology-modeled stmctures that were used in our docking calculations. The quality of the modeled receptor...

Figure 3 Quality of the docking models submitted to CAPRI. Quality criteria f nat, L rms, and I rms are estimated by comparing a model with the target X-ray structure. As described in Section Evaluation Criteria , f nat measures the recall of the native residue-residue contacts at the interface L rms and I rms are root-mean-square displacement of the backbone atoms calculated for the ligand protein after superposing the receptor (L rms) or for the interface residues only (I rms). The values of all three parameters define the quality of the model as high, medium, acceptable, or incorrect, as represented in the figure. See Refs. 63 and 105 for the exact application of these criteria.

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