Selection of screens for three-dimensional substructure searching

Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

“…Our initial studies of 3D substructure searching focused on the design of a screening system to permit rapid searching of large databases [13,14]. Given that pharmacophores are normally expressed in terms of inter-atomic distances, the screens that we developed consisted of a pair of atoms together with an associated inter-atomic distance range.…”

Searching for pharmacophoric patterns in databases of three‐dimensional chemical structures

“…This list is progressively sub-divided into a set of partitions such that each partition contains approximately the same number of fragment occurrences; the range of atom-pairs and inter-atomic distances within each of the resulting partitions then defines an individual screen (Cringean et al, 1990). This algorithm is extremely fast in operation and is also completely general in nature, since it can be applied to any sorted list of descriptor types that is to be used for indexing purposes; indeed, our implementation was developed from an earlier algorithm that was used for partitioning textual dictionaries (Cooper et al, 1980;Cooper and Lynch, 1984).…”

“…It was, however, complex in operation and required the specification of several parameter values before a screen set could be generated that demonstrated the requisite equifrequency characteristics. An alternative frequency-based selection algorithm was described later by Cringean et al (1990). This algorithm is markedly simpler in concept and gives the user a much greater degree of control over the size of the screen set that is produced, while still achieving high levels of screenout in pharmacophoric-pattern searches.…”

“…The paper concludes with some thoughts on areas for future research. In a review paper such as this it is possible to give only the main results of the work that has been carried out, and the reader is referred to the original papers (Bath et al, 1994;Brint and Willett, 1987a, 1987bClark et al, 1991Clark et al, , 1992Clark et al, , 1993Clark et al, , 1994Cringean et al, 1990;Downs et al, 1988Downs et al, , 1994Jakes et al, 1987;Jakes and Willett, 1986;Pepperrell et al, 1990Poirrette et al, , 1993 for detailed accounts of the many studies that are summarized here. More general reviews of 3D searching are provided by Bures et al (1994a), Martin et al (1990) and .…”

An Information‐Theoretic Approach to Descriptor Selection for Database Profiling and QSAR Modeling

“…Considering this task, variability or frequency analysis could be related to entropy calculations, at least in principle, which suggested to us the design and implementation of a suitable entropybased approach. About a decade ago, relative entropy calculations were first introduced in chemical database analysis to study angle and distance ranges of compounds or to establish the frequency of occurrence of substructures [3,4]. However, we focused our attention on some informationtheoretic approaches, since they were thought to be most suitable for systematic and large-scale comparison of descriptor variability.…”