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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 12 June 2012, Vol.109(24), pp.E1540-7
    Description: A new de novo protein structure prediction method for transmembrane proteins (FILM3) is described that is able to accurately predict the structures of large membrane proteins domains using an ensemble of two secondary structure prediction methods to guide fragment selection in combination with a scoring function based solely on correlated mutations detected in multiple sequence alignments. This approach has been validated by generating models for 28 membrane proteins with a diverse range of complex topologies and an average length of over 300 residues with results showing that TM-scores 〉 0.5 can be achieved in almost every case following refinement using MODELLER. In one of the most impressive results, a model of mitochondrial cytochrome c oxidase polypeptide I was obtained with a TM-score 〉 0.75 and an rmsd of only 5.7 Å over all 514 residues. These results suggest that FILM3 could be applicable to a wide range of transmembrane proteins of as-yet-unknown 3D structure given sufficient homologous sequences.
    Keywords: Mutation ; Membrane Proteins -- Chemistry
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Diabetes, July 2012, Vol.61(7), pp.1653-5
    Description: Diabetes has been associated not only with subtle cognitive deficits in mental speed and flexibility (1,2) but also with an increased risk for development of significant disruption in cognitive function in the form of dementia (3). In order to prevent subtle cognitive sequelae and potentially reduce the burden of dementia on an aging world population (4), a better understanding of the pathophysiological mechanisms underlying the cognitive dysfunction in diabetes is needed. There are several factors associated with diabetes and its management beyond acute metabolic or vascular insults that are potentially involved in this cognitive disruption, a few of which will be briefly reviewed here. Hyperglycemia may affect cognitive function by altering synaptic plasticity in the brain (5), increasing levels of oxidative stress (6), and/or subtly altering the cerebral microvasculature (7). Treatment of diabetes may lead to slight or occasionally more severe periods of hypoglycemia, which may translate to structural and metabolic alterations of the central nervous systems and subsequent cognitive dysfunction. However, it has been observed that subtle diabetes-related cognitive changes are associated with chronic hyperglycemia rather than episodes of hypoglycemia (8). The same study also observed that there was no significant difference in cognitive function between aggressively managed subjects with reduced levels of microvascular complications and those with a greater degree of microvascular complications. Other studies have observed this as well (9). This may indicate that the association between chronic hyperglycemia and subtle cognitive dysfunction is related to factors outside of microvascular complications alone. In this context, the potential impact of chronic exposure to endogenous or exogenous insulin above the normal physiological range should be critically evaluated. Mild cognitive impairment is associated not only with age of diabetes onset and disease duration but also with insulin treatment (10). The risk of dementia is also highest in people …
    Keywords: Cerebral Cortex -- Physiology ; Cerebral Small Vessel Diseases -- Physiopathology ; Cognition -- Physiology ; Diabetes Mellitus, Type 1 -- Physiopathology ; Diabetic Angiopathies -- Physiopathology ; Nerve Net -- Physiopathology
    ISSN: 00121797
    E-ISSN: 1939-327X
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  • 3
    Language: English
    In: Science, 21 November 2003, Vol.302(5649), pp.1347-1348
    Description: Structural biologists have spent decades pondering the protein-folding problem, which seeks to explain how a simple string of amino acids self- assembles into a complex three-dimensional folded protein. In his Perspective, Jones explores progress in this arena, discussing the leap forward made by Kuhlman et al. These investigators have designed a protein from scratch on the computer and then synthesized and analyzed it in atomic detail using x-ray crystallography and NMR spectroscopy. The synthesized version of their new protein matches the computer prediction, representing a big step forward for the field of structural biology.
    Keywords: Applied sciences -- Applied physics -- Photonics ; Physical sciences -- Physics -- Condensed matter physics ; Physical sciences -- Chemistry -- Chemical compounds ; Applied sciences -- Engineering -- Optical engineering ; Physical sciences -- Physics -- Mechanics ; Applied sciences -- Engineering -- Optical engineering ; Physical sciences -- Physics -- Condensed matter physics ; Mathematics -- Pure mathematics -- Linear algebra ; Physical sciences -- Physics -- Microphysics
    ISSN: 00368075
    E-ISSN: 10959203
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  • 4
    Language: English
    In: Biophysical Journal, 16 February 2016, Vol.110(3), pp.555a-555a
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.bpj.2015.11.2969 Byline: Elliot Drew, David T. Jones, B.A. Wallace Author Affiliation: (1) Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom (2) Computer Science, University College London, London, United Kingdom Article Note: (miscellaneous) 2738-PosB115
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 5
    Language: English
    In: PLoS ONE, 01 January 2014, Vol.9(3), p.e92197
    Description: The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm--FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target proteins, up to 266 amino acids in length, we are able to address the effectiveness and some limitations of such approaches to globular proteins in practice. Overall we find that using fragment assembly with both statistical potentials and predicted contacts is significantly better than either statistical potentials or contacts alone. Results show up to nearly 80% of correct predictions (TM-score ≥0.5) within analysed dataset and a mean TM-score of 0.54. Unsuccessful modelling cases emerged either from conformational sampling problems, or insufficient contact prediction accuracy. Nevertheless, a strong dependency of the quality of final models on the fraction of satisfied predicted long-range contacts was observed. This not only highlights the importance of these contacts on determining the protein fold, but also (combined with other ensemble-derived qualities) provides a powerful guide as to the choice of correct models and the global quality of the selected model. A proposed quality assessment scoring function achieves 0.93 precision and 0.77 recall for the discrimination of correct folds on our dataset of decoys. These findings suggest the approach is well-suited for blind predictions on a variety of globular proteins of unknown 3D structure, provided that enough homologous sequences are available to construct a large and accurate multiple sequence alignment for the initial contact prediction step.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: American Diplomacy, March 21, 2011
    Keywords: Secretaries Of State -- Speeches, Lectures And Essays ; Diplomacy -- Speeches, Lectures And Essays
    ISSN: 1094-8120
    Source: Cengage Learning, Inc.
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  • 7
    Language: English
    In: American Diplomacy, June 27, 2011
    Keywords: International Security -- Management ; Secretaries Of Defense -- Speeches, Lectures And Essays ; United States Foreign Relations -- Military Aspects
    ISSN: 1094-8120
    Source: Cengage Learning, Inc.
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  • 8
    Article
    Article
    Language: English
    In: American Diplomacy, August 8, 2011
    Keywords: Secretaries Of State -- Speeches, Lectures And Essays ; Indian Foreign Relations -- Economic Aspects ; United States Foreign Relations -- Economic Aspects
    ISSN: 1094-8120
    Source: Cengage Learning, Inc.
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  • 9
    Article
    Article
    Language: English
    In: American Diplomacy, July 25, 2011
    Keywords: Russian Foreign Relations -- Military Aspects ; International Security -- Management
    ISSN: 1094-8120
    Source: Cengage Learning, Inc.
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  • 10
    Article
    Article
    Language: English
    In: International Journal, June 2012, Vol.67(2), pp.527-540
    Description: Where do we draw the line on the adage that "good fences make good neighbours?" The iconic Robert Frost verse is much quoted, but do longer, higher, barbed-wire, electrified, security-patrolled, and access-controlled fences make for still better neighbours? This question embodies the essence of current continuing tensions along the Canadian-US borders. The traditional "longest undefended cliche" is quickly becoming a 20th-century artefact with levels of security and proposals for much, much more than would have been conceivable a decade ago, before 11 September 2001. Admittedly, this circumstance would barely be recognized as a constraint, let alone a problem, throughout much of the world in historical or even current terms, where crossing a national border is a serious personal-political decision. (Try getting a visa to Russia or China if you want a lesson in bureaucratic frustration.) Nevertheless, due to the unique US-Canadian relationship, its recent evolution needs examination. Adapted from the source document.
    Keywords: History & Archaeology ; International Relations
    ISSN: 0020-7020
    E-ISSN: 2052-465X
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