MACCS representation

CATS, CATS3D, SURFCATS, MACCS) and three molecular representations (full, scaffold and reduced scaffold representation). 

Fig. 3.5 Averaged enrichment factors over 10 ligand classes from the COBRA database (top 5%). Comparison of the performances of MACCS, CATS, CATS3D and SURFCATS for full molecular representations, scaffolds (Sc)...

The internal representation of molecules is accomplished using the technique developed by Wipke and Dyott (3), and later used by Molecular Design Limited (MDL) in several of their commercial programs. An MDL program, MACCS, is used to graphically input the molecular structure of the compound of interest, then save that structure into a file (molfile). The importation of this file provides CHESS with information such as the number and type of atoms and bonds, as well as stereochemical information. 

The number of features combined in a vector-type representation is indicative of the dimensionality of the problem space. Low-dimensional representations, on the one hand, allow easy visualization but are most often not very discriminative. Highdimensional representations, on the other hand, such as those encoded in Daylight fingerprints [23], MACCS keys [24], or UNITY fingerprints [25], provide more detailed accounts on structural or chemical variations. However, this is achieved at the cost of visualization. Part of these high-dimensional representations describe specific local features of molecules, and because not all molecules in the data contain these features, gaps or zeros are introduced in the data representation. For certain data mining methods, this could be problematic. In many cases, dimensionality reduction procedures are applied to reduce the complexity of the representation. The reduction of the dimensionality is accomplished by means of 1) variable selection procedures, 2)... 

The chemical structure files built by these software packages consist of connection tables, a form of structural representation used in the CAS Chemical Registry System, and in consequence by both CAS ONLINE and DARC, and incidentally in many other systems (including MACCS). Both CPSS and PSIDOM include modules for building chemical structure data bases on personal computers which, in the case of PSIDOM, are limited only by the capacity of the disk storage... 

Anderson, S. Graphical Representation of Molecules and Substructure Search Queries in MACCS. J. Mol. Graphics 1984, 2, 83-90. 

How does this example apply to the use of multiple similarity methods Each of the similarity methods can be considered to be equivalent to an independent judge, since none of the values produced by the other methods have an explicit impact on the value produced by a given method. This may not always be the case, for example, if two methods use MACCS key fingerprints, but one uses the Tanimoto (Jacard) and the other a closely related similarity function (see Table 15.3). As shown by Gower [76], some molecular similarity functions are monotonically related. Thus, comparisons of these functions based on the same molecular representation will produced linear correlations of the values computed by the two functionally similarity functions. Hence, only one of the functions should be used. 

Figure 1.9 shows examples of CSs constructed with respect to four different binary FP representations using the similarity-based PCA procedure described in the previous sectioa The first two examples are based on atom pair and MACCS key FPs that were discussed in some detail in Sect. 1.2.1.1. Of the latter two, both... 

We have therefore introduced the notion of an SGroup as an extension to chemical structure representation, and have implemented SGroups in a MACCS-II... 

In MACCS-II this representation is in the form of a Molfile. Extensions have been added to the Molfile description that allow SGroup information to be stored and transferred to other programs. 

In the arena of chemical structure management, MDL (then in Hayward, California) was dominant. This company, which was founded in 1978 by Prof. Todd Wipke and others, marketed a program called MACCS for management of databases of compounds synthesized at or acquired by pharmaceutical companies. The software stored chemical structures (in two-dimensional representation) and allowed substructure searching and later similarity searching. 

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