Tweak algorithm

Kilvington and Leach have applied the random tweak algorithm to determine which of a series of possible acyclic linkers (determined randomly or systematically) is suitable to connect two isolated ligand fragments. The random tweak method is used to determine the amount of rotation each bond must undergo to match die ends of a flexible chain to the isolated fragments. ... 

For STRIPS-like operators. Chapman (1985) developed a polynomialtime algorithm, called TWEAK, around five actions that are necessary and sufficient for constructing a correct and complete plan. As soon as we try to extend these ideas to nonmonotonic planning with conditional operators, we realize that no polynomial-time algorithm can be constructed, as the following theorem explicitly prohibits (Chapman, 1985) ... 

CombiDock Tweaks the DOCK algorithm to identify suitable scaffold orientations in the binding pocket. Proceeds using the seed and grow approach to design combinatorial libraries (73)... 

Another optimization method, related to the least-squares fitting used in point-based algorithms, is the directed tweak method [31]. This is a torsional space optimizer, in which the rotatable bonds of the ligands are adjusted at search time to produce a conformation which matches the 3D query as closely as possible. As directed tweak involves the use of analytical derivatives, it is very fast and allows for an RMS fit to consider ligand flexibility. 

Alignment methods are also known to combine different optimization methods, such as a genetic algorithm and a directed tweak method [36]. 

Methods that combine a search technique with other optimization approaches include distance geometry, random search, and genetic algorithms. A comparison of these methods with derivative-based optimization concluded that all were inferior in performance to directed tweak, with the most favorable of the three being the genetic algorithm. ... 

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