Similarity searching on CAS Registry substances. 2. 2D structural similarity

Fisanick, William; Lipkus, Alan H.; Rusinko, Andrew

doi:10.1021/ci00017a016

Cited by 34 publications

(24 citation statements)

References 8 publications

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“…[13][14][15] The 2D studies involved subsets of the substructural fragments that comprise the CAS Online screen dictionary, 16 focusing on the different types of similarity relationships that can be identified between a target structure and a database structure when different classes of substructural fragment are employed. For example, the selection of augmented atoms (an atom and its pendant atoms and bonds) and atom sequences (unbranched chains of atoms) gives a very different view of the structural resemblances between a pair of molecules from that provided by the selection of ring composition fragments (the atoms within a ring and the bonds between them).…”

Section: Fragment-based Similarity Searchingmentioning

confidence: 99%

Chemical Similarity Searching

Willett

and

Downs

1998

J. Chem. Inf. Comput. Sci.

1,636

1,643

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This paper reviews the use of similarity searching in chemical databases. It begins by introducing the concept of similarity searching, differentiating it from the more common substructure searching, and then discusses the current generation of fragment-based measures that are used for searching chemical structure databases. The next sections focus upon two of the principal characteristics of a similarity measure: the coefficient that is used to quantify the degree of structural resemblance between pairs of molecules and the structural representations that are used to characterize molecules that are being compared in a similarity calculation. New types of similarity measure are then compared with current approaches, and examples are given of several applications that are related to similarity searching.

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Section: Fragment-based Similarity Searchingmentioning

confidence: 99%

Chemical Similarity Searching

Willett

and

Downs

1998

J. Chem. Inf. Comput. Sci.

1,636

1,643

View full text Add to dashboard Cite

show abstract

“…To solve this problem, a similarity analysis between clusters must be introduced. The procedure uses the so‐called Tanimoto analysis 31, 32 to evaluate similarity among molecular arrangements to discard redundant degeneracy. This procedure calculates similarity between structures pair by pair.…”

Section: Systems and Computational Detailsmentioning

confidence: 99%

Multiple minima hypersurfaces studies of aluminosilicate hydration

Pérez-Badell

Montero

2009

Int J of Quantum Chemistry

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Hydrothermal zeolite synthesis is a complex process that is difficult toanalyze experimentally. In this work, the role of water as solvent on the formation of aluminate and aluminosilicate clusters is described by quantum chemical calculations. The multiple minima hypersurfaces approach was used. It combines quantum chemical Hamiltonians for the calculation of the internal energy with statistical modeling and formulae for the calculation of thermodynamic functions of association. The structures of most probable hydration clusters are proposed and some of their association properties are calculated. Ab initio and semiempirical calculations of the structures and relevant reactions of aluminate and aluminosilicate fragments were reported. The results could be employed for an interpretation of the aluminosilicate synthesis. Calculations demonstrate the importance of considering other than the deepest minimum structures, giving a significant role to consider entropy of association.

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“…In this method, entire substructures, according to some defined scheme, are collapsed into single nodes resulting in an RG that is smaller and less complex. RGs were first developed for application in generic chemical structure retrieval using structure and substructure searching, but have since been applied to similarity searching [34][35][36][37].…”

Section: Reduced Graphsmentioning

confidence: 99%

On Scaffolds and Hopping in Medicinal Chemistry

Brown

Jacoby²

2006

MRMC

139

130

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The molecular scaffold is an oft-cited concept in medicinal chemistry suggesting that the definition of what makes a scaffold is rigorous and objective. However, this is far from the case with the definition of a scaffold being highly dependent on the particular viewpoint of a given scientist. It follows, therefore, that the definition of scaffold hopping and, more importantly, the detection of what constitutes a scaffold hop, is also ill-defined and highly subjective. Essentially, it is agreed that scaffolds should be substantially different from each other, although significantly similar to each other, to constitute a hop. In the latter, the scaffolds must permit a similar geometric arrangement of functional groups to permit the mode of action. However, this leaves the paradox of how to describe both scaffold similarity and dissimilarity simultaneously. In this paper, the current statuses of scaffolds and scaffold hopping are reviewed based on published examples of scaffold hopping from the literature. An investigation of the degree to which it is possible to formulate a more rigorous definition of scaffolds and hopping in the context of molecular topologies is considered. These techniques are adapted from chemoinformatics to be applied in the design of new medicinal compounds.

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Similarity searching on CAS Registry substances. 2. 2D structural similarity

Cited by 34 publications

References 8 publications

Chemical Similarity Searching

Chemical Similarity Searching

Multiple minima hypersurfaces studies of aluminosilicate hydration

On Scaffolds and Hopping in Medicinal Chemistry

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