Scoring functions penalty terms

In the derivation of regression-based empirical scoring schemes, on the other hand, penalty terms have traditionally not been included. However, some situations like obvious electrostatic and steric clashes can be avoided by guessing reasonable penalty terms or by importing them from molecular mechanics force fields. An example of this is the chemical scoring function available in the docking program This function is a modified van... 

Constraints are typically applied as a penalty function that is added as an extra term in the scoring function, often as some simple function (e.g., harmonic) of the difference between the actual and target values. Other strategies are possible, however, and constraints have also been used systematically in the construction of model structures. This can be applied to distance constraints, where a buildup procedure is used to generate stmctures that satisfy all constraints [64]. Angle constraints can also be used to systematically search the conformational space, both using a branch-and-bound procedure [65] or in a tree-search algorithm in combination with distance constraints [66]. 

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