Volume 2 Chapter 2 2D-Constrain Sub-menu DEFINE-STRUCTURE

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DICE is used to select the Dice Coefficient for similarity searching.


Similarity searching involves the comparison of an input connectivity record, referred to as the query, with the connectivity records of every entry in the database, the targets.

A quantitative measure of the similarity between the query and each of the targets can be calculated. This measure is known as a similarity coefficient. The procedure implemented within QUEST and QUEST3D is based on the work reported by Willett et al. (J.Chem.Inf.Comput.Sci. 26,36,1986).

The similarity coefficient is derived from the chemical connectivity bit screens (bits 249-682 in Appendix 1) of the query structure and each of the target structures.

A variety of similarity coefficients can be used to express the similarity between two bit-maps of equal length and a full discussion is presented by B.Everitt (Cluster Analysis; Halsted-Heinemann:London, 1980).

Two similarity coefficients are available in QUEST and QUEST3D:

the Dice coefficient
the Tanimoto coefficient (also known as the Jaccard coefficient) - this is the default.

= the number of bit screens set in the query structure
= the number of bit screens set in the target structure
= the number of bit screens which are common to both the query and target structures.

The Dice coefficient is: D= 2Nc/(Nq+Nt)

The Tanimoto coefficient is: T= Nc/(Nq+Nt-Nc)

Related commands


See also Vol. 1, Chapter 6.

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Volume 2 Chapter 2 2D-Constrain Sub-menu Display of Atom and Bond Pproperies.