Vector correlation

Linear representations are by far the most frequently used descriptor type. Apart from the already mentioned structural keys and hashed fingerprints, other types of information are stored. For example, the topological distance between pharmacophoric points can be stored [179, 180], auto- and cross-correlation vectors over 2-D or 3-D information can be created [185, 186], or so-called BCUT [187] values can be extracted from an eigenvalue analysis of the molecular adjacency matrix. 

Fechner U, Lutz F, Renner S, Schneider P, Scheider G. (2003) Comparison of Correlation Vector Methods for Ligand-Based Similarity Searching. /. Comput.-Aided Mol. Des. 17 687-698. 

Lowry, D. F., Correlated Vector Mode of Multiple-Spin Systems, Concepts in Magnetic Resonance An Educational Journal, 1994, 6 (No I)... 

Alignment-free Pharmacophore Patterns -A Correlation-vector Approach ... 

Fig. 3.1 The CATS family of descriptors CATS, CATS3D and SURFCATS. The degree of abstraction from the atomic molecular structure is assumed to be SURFCATS > CATS3D > CATS. All descriptors are based on a PPP-type description of the underlying molecule. For each descriptor, pairs ofPPPs are transformed into a correlation vector. CATS is calculated from the topological...

The main difference in the correlation vector representation of a 3D conformation in comparison with a topological representation of a molecule is that the distances between the atoms are no longer shortest paths. Instead, Euclidean distances between all atoms are used. Distances between atoms are not restricted to integer values, so the distances have to be partitioned into a set of... 

The first application of a surface-based pharmacophore correlation vector was reported by Stiefl and Baumann in 2003 [18] with the MaP (mapping property distributions of molecular surfaces) descriptor. They applied their MaP descriptor for QSAR applications. To our knowledge, an application of this descriptor to similarity searching has not been reported. 

Which influence do different scaling methods have on the performance of the topological CATS descriptor We addressed this question with a comparison of three different ways of scaling the correlation vector descriptor [38] ... 

Fig. 3.11 Comparison of the correlation vectors of a SQUID COX-2 pharmacophore model and the CATS3D correlation vectors of the three molecules used for the calculation of the pharmacophore model.

In a growing number of studies, correlation-vector representations of pharmaco-phoric features of molecules have been proven to be useful in similarity searching and de novo design projects. They allow for rapid database screening, which... 

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