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The Geminiviridae is an extensive family of plant viruses responsible for economically devastating diseases in crops worldwide. Geminiviruses package circular, single-stranded DNA (ssDNA) genomes. The characteristic twinned or "geminate" particles, which consist of two joined, incomplete T = 1 icosahedra, are unique among viruses. We have determined the(More)
The complete nucleotide sequence of the middle component RNA (M RNA) of the comovirus bean pod mottle virus (BPMV) has been determined. The sequence consists of 3662 nucleotides and contains a single long open reading frame sufficient to code for a protein of 113,353 Da. The proteolytic processing sites within this protein have been identified by comparison(More)
Conventional similarity searching of molecules compares single (or multiple) active query structures to each other in a relative framework, by means of a structural descriptor and a similarity measure. While this often works well, depending on the target, we show here that retrieval rates can be improved considerably by incorporating an external framework(More)
We present a workflow that leverages data from chemogenomics based target predictions with Systems Biology databases to better understand off-target related toxicities. By analyzing a set of compounds that share a common toxic phenotype and by comparing the pathways they affect with pathways modulated by nontoxic compounds we are able to establish links(More)
BACKGROUND High-resolution MRI has been shown to be capable of identifying plaque constituents, such as the necrotic core and intraplaque hemorrhage, in human carotid atherosclerosis. The purpose of this study was to evaluate differential contrast-weighted images, specifically a multispectral MR technique, to improve the accuracy of identifying the(More)
Target identification is a critical step following the discovery of small molecules that elicit a biological phenotype. The present work seeks to provide an in silico correlate of experimental target fishing technologies in order to rapidly fish out potential targets for compounds on the basis of chemical structure alone. A multiple-category(More)
Different molecular descriptors capture different aspects of molecular structures, but this effect has not yet been quantified systematically on a large scale. In this work, we calculate the similarity of 37 descriptors by repeatedly selecting query compounds and ranking the rest of the database. Euclidean distances between the rank-ordering of different(More)
Capsaicin and resiniferatoxin are natural products which act specifically on a subset of primary afferent sensory neurons to open a novel cation-selective ion channel in the plasma membrane. These sensory neurons are involved in nociception, and so, these agents are targets for the design of a novel class of analgesics. Although synthetic agonists at the(More)
In silico target fishing is an emerging technology that enables the prediction of biological targets of compounds on the basis of chemical structure by using information from increasingly available biologically annotated chemical databases. We provide a comparative review of recent studies in which data mining, similarity, or docking of chemical structures(More)
High-throughput screening (HTS) plays a pivotal role in lead discovery for the pharmaceutical industry. In tandem, cheminformatics approaches are employed to increase the probability of the identification of novel biologically active compounds by mining the HTS data. HTS data is notoriously noisy, and therefore, the selection of the optimal data mining(More)