Manual docking

Manual docking P450terp, P450cam, P450BM3 (140) 2D6 Jones et al. 1998 (134)... 

Fig. 5. Models of the receptor-G protein complex. Two representations of receptor-G protein complexes are shown. The R Ga(0) fly complex created by manually docking the G protein onto an activated receptor model based on the rhodopsin crystal structure (1GZM) (left panel). Sites on Got that cross-link to residue S240 (cyan sphere) on the receptor are highlighted (cyan). This sort of data will be critical for improving models of the receptor-G protein complex, as it provides constraints for the location of IC 3 relatively to Ga. In this model, the nucleotide-binding pocket is some 30 A away from the receptor-binding surface. The model of an Ro Ga (O) [jy-com pIex is based on coordinates generously provided by K. Palczewski (published in Fotiadis et al, 2004).

Catalytic site prediction using manual docking in combination with energy minimizations and/or MD simulations. 

Figure 17.8 (a) Active site found in CYP2C8 (b) taxol manually docked in CYP2C8 showing key interaction residues. 

Figure 17.13 CYP2D6 with (a) debrisoquine and (b) metroprolol manually docked into the active site. Constraints were applied between the heme oxygen and the known metabolic sites. Both substrates can bind to asp301 and interact with phe120 and phe483. (c) Debrisoquine docked into a substrate recognition site showing interactions with...

Figure 17.17 Phenobarbital manually docked into the CAR crystal structure.

Figure 1.2 Comparison of high-resolution (b-i) and medium-resolution (a) structures of ABC proteins. The predicted transmembrane regions are indicated by the pink bounda for a)-(f). (a) Medium-resolution model of P-gp with a-helices placed in elongated elements identified in the EM map [110], NBDs are based on the MJ0796 structure [87] that was manually docked into a bilobed density in the appropriate region of the medium-resolution 3D map. (b) Savl866...

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