ADAM docking

ADAM DOCK FlexX Hammerhead MCDOCK SANDOCK... 

A local induced fit motion is sampled by ADAM docking in combination with an energy minimization. ADAM utilizes a vdW-offset 3D grid. To enlarge the pocket uniformly, the potential curve is shifted that allows the atoms to get closer. The stmcture optimization covers side chains and ligand movements. The energy minimization is performed with the L-BFGS method [74]. 

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. 

Perhaps the most commonly utilized systematic search method is incremental construction, which is used by DOCK [41], FlexX [42], E-Novo [91], LUDI [45, 46], ADAM [92], and TrixX [93]. In this particular method, the ligand is... 

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