Chemical scoring function

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... 

Speed. Given the growth in the size of corporate and research chemical databases, a scoring function must be computable in less than 2 min of CPU time to be useful. 

Since its first introduction in 1982, the DOCK software has been extended in several directions. The matching spheres can be labeled with chemical properties,61 and distance bins are used to speed up the search process.62,63 Recently, the search algorithm for distance-compatible matches was changed28 to the clique-detection algorithm introduced by Crippen and co-workers.55 Furthermore, several scoring functions are now applied in combination with the DOCK algorithm.64-68... 

In addition, there have also been a number of efforts to find more efficient ways to categorise and enumerate compounds. One approach to defining the relationship of compounds to each other uses a chemical space defined by a set of 500 compounds described with 60 molecular descriptors onto which novel compounds can then be mapped.116 Another approach that has been described uses a rule-based classification scheme to define the common scaffold or core of compounds.117 This approach has been taken further to develop a scoring function to allow the prioritisation of compound libraries for testing.118... 

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