Other Docking Algorithms

Fie Edit Select 3D Gretirics Disiiev Color Compute Hydrogen Bond Giid30 Help 

It gives the protein-binding affinity in kilocalorie per mole (kcal/mol) for every conformation and also the RMSD. automatically detects the processors and displays it. The log files and output files can be seen in the folder. The outfile (out.pdbqt) can be visualized through PyMOL [16] or AutoDock tools (Figs. 4.49 and 4.50). 

In PyMOL, we can visualize all the conformations by clicking on the arrow button or the play button. 

Ludi Ludi [17] is a product of Acceliys (Insight II) which can be used in both stmc-ture-based dmg design (protein structure is known) and ligand-based drug design (protein stmcture is not known). Based on this, it mns in two modes receptor mode and active analog mode. This mainly follows the fragment approach where initially 

FiI9 Edit S l cl 3D Qtiphici Display Colpr Campula Hydragtn Bonds GridJD 

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Other docking algorithms such as Glide [33], Dock [34] and GOLD [35] have also been used to predict the site of metabolism, and a recent study compared the performance of multiple algorithms in the field of cytochrome P450s [36],... 

While the initial DOCK algorithm uses volume as the feature to be matched, other approaches use chemical interactions. Mizutani et al. [34] presented the program ADAM in which hydrogen bonding is the feature used for matching. Possible matchings are enumerated and filtered based on distance compatibility. 

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