Similarity-based virtual screening using 2D fingerprints

This paper summarises recent work at the University of Sheffield on virtual screening methods that use 2D fingerprint measures of structural similarity. A detailed comparison of a large number of similarity coefficients demonstrates that the well-known Tanimoto coefficient remains the method of choice for the computation of fingerprint-based similarity, despite possessing some inherent biases related to the sizes of the molecules that are being sought. Group fusion involves combining the results of similarity searches based on multiple reference structures and a single similarity measure. We demonstrate the effectiveness of this approach to screening, and also describe an approximate form of group fusion, turbo similarity searching, that can be used when just a single reference structure is available

Elite Tweets: Analysing the Twitter Communication Patterns of Labour Party Peers in the House of Lords

The micro-blogging platform Twitter has gained notoriety for its status as both a communication channel between private individuals, and as a public forum monitored by journalists, the public, and the state. Its potential application for political communication has not gone unnoticed; politicians have used Twitter to attract voters, interact with constituencies and advance issue-based campaigns. This article reports on the preliminary results of the research team’s work with 21 peers sitting on the Labour frontbench. It is based on the monitoring and archival of the peers’ activity on Twitter for a period of 100 days from 16th May to 28th September 2012. Using a sample of more than 4,363 tweets and a mixed methodology combining semantic analysis, social network analysis and quantitative analysis, this paper explores the peers’ patterns of usage and communication on Twitter. Key findings are that as a tweeting community their behavior is consistent with others, however there is evidence that a coherent strategy is lacking. Labour peers tend to work in ego networks of self-interest as opposed to working together to promote party polic

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Next-to-leading order QCD corrections to Higgs boson production in association with a photon via weak-boson fusion at the LHC

Higgs boson production in association with a hard central photon and two forward tagging jets is expected to provide valuable information on Higgs boson couplings in a range where it is difficult to disentangle weak-boson fusion processes from large QCD backgrounds. We present next-to-leading order QCD corrections to Higgs production in association with a photon via weak-boson fusion at a hadron collider in the form of a flexible parton-level Monte Carlo program. The QCD corrections to integrated cross sections are found to be small for experimentally relevant selection cuts, while the shape of kinematic distributions can be distorted by up to 20% in some regions of phase space. Residual scale uncertainties at next-to-leading order are at the few-percent level.Comment: 17 pages, 7 figures, 1 tabl

Distributed Implementation of SIGNAL: Scheduling & Graph Clustering

International audienceThis paper introduces the scheduling strategy and some key tools which have been designed for the distributed implementation of Signal, a real-time synchronous dataflow language. First, we motivate a scheduling strategy with respect to the reactivity and time-predictability requirements bound to real-time computing. Then, several key tools to implement this scheduling strategy are described. These tools are acting on the concept of Synchronous-Flow Dependence Graph (SFD Graph) which defines a generalization of Directed Acyclic Graph and constitutes the abstract representation of Signal programs. The tools presented in this paper are: (a) the abstraction of SFD graphs which enables grain-size tuning according to the target architecture, (b) the notion of scheduling over SFD graphs and (c) qualitative clustering tools based on the notion of Compositional Deadlock Consistency