Geoffrey M. Downs

Chemical Similarity Searching

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.

Review of ring perception algorithms for chemical graphs

Current ring perception algorithms for use on chemical graphs concentrate on processing specific structures. In this review, the various published ring perception algorithms are classified according to the initial ring set obtained, and each algorithm or method of perception is described in detail. The final ring sets obtained are discussed in terms of their suitability for use in representing the ring systems in structurally explicit parts of generic chemical structures.

Chemical Fragment Generation and Clustering Software

Barnard Chemical Information Ltd.s software products for generation of fragment-dictionary-based chemical structure fingerprints and for hierarchical and nonhierarchical clustering of large files of structures are described.

Techniques for Generating Descriptive Fingerprints in Combinatorial Libraries

One of the problems encountered in handling computer representations of combinatorial libraries (especially “virtual libraries”) is the extremely large number of compounds which may be covered by even quite simple libraries. This paper discusses work on the generation of structure fingerprints for the compounds in a library, which avoids the need to enumerate the compounds themselves by utilizing techniques originally developed for handling Markush structures in chemical patents.

Theoretical aspects of ring perception and development of the extended set of smallest rings concept

This paper considers the problems associated with processing planar (two-dimensional) representations of three-dimensional structures. To overcome the ambiguity of such representations, a new ring set is defined in terms of simple faces and cut faces. The concept of a cut-vertex graph is introduced to explain the combinatorial relationship between the number of simple faces and the number of planar embedments

Chemical patent information systems

The chemical structure information in patents remains difficult to access, partly because it is frequently expressed in the form of Markush structures, which can encompass enormous numbers of individual compounds. Early search systems were based on chemical ‘fragment codes’ that have still not been entirely superseded by the ‘topological’ systems developed during the 1980s.

Transputer implementations of chemical substructure searching algorithms

Abstract Two chemical substructure searching algorithms, the relaxation algorithm and the set reduction algorithm, are introduced and described. Transputer based serial implementations of both are compared for performance; the relaxation algorithm is shown to be both more effective and more efficient. Strategies are discussed for multi-transputer implementations of the relaxation algorithm. Experimental results show that near-linear speedups are obtained with networks containing up to 21 transputers.

Computer Storage and Retrieval of Generic Chemical Structures in Patents. 9. An Algorithm To Find the Extended Set of Smallest Rings in Structurally Explicit Generics

This paper reports how Zamoras smallest set of smallest rings algorithm has been modified and extended to provide an algorithm that will find the extended set of smallest rings (ESSR) for specific and structurally explicit generic structures. Modifications are necessary to find the ESSR rings within a partial structure connection table, while extensions are required to perceive the ESSR rings that span several such connection tables. Particular care is involved when structures containing primary cut faces or alternative embedments are processed

The Use of Similarity and Clustering Techniques for the Prediction of Molecular Properties

The fine chemicals industry makes extensive use of systems for the storage and manipulation of chemical structure information. The primary function of these systems is to provide facilities for storage and retrieval, but the close relationship that is known to exist between the structure of a molecule and its physical, chemical and biological properties has led to increasing interest in the use of chemical structure databases for the prediction of molecular properties.

Computer storage and retrieval of generic chemical structures in patents. 10. Assignment and logical bubble-up of ring screens for structurally explicit generics

The rings perceived within and across the partial structures of structurally explicit generics are analyzed to produce ring-screen information that complements the existing fragment screens. This paper presents and discusses the format of these ring screens. The resultant bit vectors for each partial structure are accumulated to retain their logical relationships by means of a «bubble-up» of the vectors. The principles of the bubble-up are outlined and explained by means of several examples