Effectiveness of retrieval in similarity searches of chemical databases: A review of performance measures

This article reviews measures for evaluating the effectiveness of similarity searches in chemical databases, drawing principally upon the many measures that have been described previously for evaluating the performance of text search engines. The use of the various measures is exemplified by fragment-based 2D similarity searches on several databases for which both structural and bioactivity data are available. It is concluded that the cumulative recall and G-H score measures are the most useful of those tested

Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings

This paper compares 22 different similarity coefficients when they are used for searching databases of 2D fragment bit-strings. Experiments with the National Cancer Institute's AIDS and IDAlert databases show that the coefficients fall into several well-marked clusters, in which the members of a cluster will produce comparable rankings of a set of molecules. These clusters provide a basis for selecting combinations of coefficients for use in data fusion experiments. The results of these experiments provide a simple way of increasing the effectiveness of fragment-based similarity searching systems

Use of the R-group descriptor for alignment-free QSAR

An R-group descriptor characterises the distribution of some atom-based property, such as elemental type or partial atomic charge, at increasing numbers of bonds distant from the point of substitution on a parent ring system. Application of Partial Least Squares (PLS) to datasets for which bioactivity data and R-group descriptor information are available is shown to provide an effective way of generating QSAR models with a high level of predictive ability. The resulting models are competitive with the models produced by established QSAR approaches, are readily interpretable in structural terms, and are shown to be of value in the optimisation of a lead series

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

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

Cultural threads in primary schools

This paper explores headteachers’ and teachers’ perceptions of foreign languages (FL) and cultural learning in three primary schools in areas of disadvantage in England. Drawing upon a new theoretical frame for primary languages – Critical Cosmopolitanism (Delanty, 2006; Beck and Sznaider, 2006) and The Grammar of Culture (Holliday, 2018), we argue that the grand narrative of a target language inhabited by a target culture is outdated and approaches to cultural learning in primary schools could lead the way. There is substantial evidence that most learners find language lessons fun, particularly activities such as songs, stories and intercultural events (Driscoll et al.,2004, 2014; Cable et al. 2010). The discourse on conditions for inclusive practice is less commonplace and little is known about FL learning in areas of high deprivation (Nikolov & Mihaljević Djigunović, 2011). Teachers and headteachers in this study were committed to cultural learning and staff adopted creative approaches to teaching. The findings, however, also indicate that traditional notions of a mono or homogenised national culture with associated stereotypes linger in teachers’ framing of FL. There exists a need for a more personalised approach to cultural learning drawing upon children’s own cultural experiences. Data was analysed thematically following strict ethical guidelines and all names were anonymised to ensure confidentiality

Analysis and design of a modular multilevel converter with trapezoidal modulation for medium and high voltage DC-DC transformers

Conventional dual active bridge topologies provide galvanic isolation and soft-switching over a reasonable operating range without dedicated resonant circuits. However, scaling the two-level dual active bridge to higher dc voltage levels is impeded by several challenges among which the high dv/dt stress on the coupling transformer insulation. Gating and thermal characteristics of series switch arrays add to the limitations. To avoid the use of standard bulky modular multilevel bridges, this paper analyzes an alternative modulation technique where staircase approximated trapezoidal voltage waveforms are produced; thus alleviating developed dv/dt stresses. Modular design is realized by the utilization of half-bridge chopper cells. Therefore, the analyzed converter is a modular multi-level converter operated in a new mode with no common-mode dc arm currents as well as reduced capacitor size, hence reduced cell footprint. Suitable switching patterns are developed and various design and operation aspects are studied. Soft switching characteristics will be shown to be comparable to those of the two-level dual active bridge. Experimental results from a scaled test rig validate the presented concept

Identification of diverse database subsets using property-based and fragment-based molecular descriptions

This paper reports a comparison of calculated molecular properties and of 2D fragment bit-strings when used for the selection of structurally diverse subsets of a file of 44295 compounds. MaxMin dissimilarity-based selection and k-means cluster-based selection are used to select subsets containing between 1% and 20% of the file. Investigation of the numbers of bioactive molecules in the selected subsets suggest: that the MaxMin subsets are noticeably superior to the k-means subsets; that the property-based descriptors are marginally superior to the fragment-based descriptors; and that both approaches are noticeably superior to random selection

Fault blocking converters for HVDC transmission : a transient behaviour comparison

A thorough comparison of the transient behaviours of two state-of-the-art converters suitable for HVDC transmission is presented. The Alternate Arm and Mixed-Cell Modular Multilevel Converter topologies both have DC fault blocking capability and are selected for the comparison. Converter performance is evaluated and compared under various transient conditions including charging sequence, unbalanced operation, and DC fault recovery. The study is conducted using high-fidelity converter simulation models, integrating detailed controllers that reflect real-scale projects. The main findings of the study assist in the selection of the most suitable converter, given specific performance specifications such as capacitor voltage ripple, cell capacitor requirements, and response during transient operation