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Pharmacophore multiplets are useful tools for 3D database searching, with the queries used ordinarily being derived from ensembles
of random conformations of active ligands. It seems reasonable to expect that their usefulness can be augmented by instead
using queries derived from single ligand conformations obtained from aligned ligands. Comparisons of pharmacophore multiplet
searching using random conformations with multiplet searching using single conformations derived from GALAHAD (a genetic algorithm
with linear assignment for hypermolecular alignment of datasets) models do indeed show that, while query hypotheses based
on random conformations are quite effective, hypotheses based on aligned conformations do a better job of discriminating between
active and inactive compounds. In particular, the hypothesis created from a neuraminidase inhibitor model was more similar
to half of 18 known actives than all but 0.2% of the compounds in a structurally diverse subset of the World Drug Index. Similarly,
a model developed from five angiotensin II antagonists yielded hypotheses that placed 65 known antagonists within the top
0.1–1% of decoy databases. The differences in discriminating power ranged from 2 to 20-fold, depending on the protein target
and the type of pharmacophore multiplet used. 相似文献
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MK Hossain-Ibrahim K Rezajooi JK MacNally MRJ Mason AR Lieberman PN Anderson 《BMC neuroscience》2006,7(1):8-21
Background
Inflammation around cell bodies of primary sensory neurons and retinal ganglion cells enhances expression of neuronal growth-associated genes and stimulates axonal regeneration. We have asked if inflammation would have similar effects on corticospinal neurons, which normally show little response to spinal cord injury. Lipopolysaccharide (LPS) was applied onto the pial surface of the motor cortex of adult rats with or without concomitant injury of the corticospinal tract at C4. Inflammation around corticospinal tract cell bodies in the motor cortex was assessed by immunohistochemistry for OX42 (a microglia and macrophage marker). Expression of growth-associated genes c-jun, ATF3, SCG10 and GAP-43 was investigated by immunohistochemistry or in situ hybridisation. 相似文献3.
The performance of a classification model is often assessed in terms of how well it separates a set of known observations into appropriate classes. If the validation sets used for such analyses are redundant due to bias in sampling, the relevance of the conclusions drawn to prospective work in which new kinds of positives are sought may be compromised. In the case of the various virtual screening techniques used in modern drug discovery, such bias generally appears as over‐representation of particular structural subclasses in the test set. We show how clustering by substructural similarity, followed by applying arithmetic and harmonic weighting schemes to receiver operating characteristic (ROC) curves, can be used to identify validation sets that are biased due to such redundancies. This can be accomplished qualitatively by direct examination or quantitatively by comparing the areas under the respective linear or semilog curves (AUCs or pAUCs). Copyright © 2009 John Wiley & Sons, Ltd. 相似文献
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The nucleide 73Kr has been identified by on-line mass separation as a precursor of β-delayed proton emission. The proton branch is (6.8 ±1.2) × 10−3 proton/decay. The protons populate the ground state and also the first excited 2+ state at 866 keV in 72Se with a relative intensity of (35±9) %. The value of QEC−Bp, where Bp is the proton separation energy for the nucleus 73Br, is found to be 4.85 ±0.30 MeV based on the fraction of proton events preceded by positron decay. 相似文献
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