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511 Newest Publications of BioMed Central

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Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

23-Nov-2015 | Maheshwari, Surabhi; Brylinski, Michal, BMC Structural Biology, 2015

Background: Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which ...

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Short-term, high-fat diet accelerates disuse atrophy and protein degradation in a muscle-specific manner in mice

04-Nov-2015 | Roseno, Steven L; Davis, Patrick R; Bollinger, Lance M; Powell, Jonathan JS; Witczak, Carol A; Brault, Jeffrey J, Nutrition & Metabolism, 2015

Background: A short-term high-fat diet impairs mitochondrial function and the ability of skeletal muscle to respond to growth stimuli, but it is unknown whether such a diet alters the ability to respond to atrophy signals. The purpose of this study was to determine whether rapid weigh gain ...

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Clustering and percolation in protein loop structures

29-Oct-2015 | Peng, Xubiao; He, Jianfeng; Niemi, Antti J, BMC Structural Biology, 2015

Background: High precision protein loop modelling remains a challenge, both in template based and template independent approaches to protein structure prediction.MethodWe introduce the concepts of protein loop clustering and percolation, to develop a quantitative approach to systematically ...

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Low-calcium diet prevents fructose-induced hyperinsulinemia and ameliorates the response to glucose load in rats

29-Oct-2015 | Voznesenskaya, Anna; Tordoff, Michael G, Nutrition & Metabolism, 2015

Background: Consuming a fructose-rich diet leads to hyperinsulinemia, impaired glucose tolerance, and insulin resistance. In humans, the consumption of high levels of refined sugars often coincides with a diet containing suboptimal levels of calcium. Calcium and carbohydrate metabolism interact, ...

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A polynomial time algorithm for computing the area under a GDT curve

26-Oct-2015 | Poleksic, Aleksandar, Algorithms for Molecular Biology , 2015

Background: Progress in the field of protein three-dimensional structure prediction depends on the development of new and improved algorithms for measuring the quality of protein models. Perhaps the best descriptor of the quality of a protein model is the GDT function that maps each distance ...

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Weight loss-induced changes in adipose tissue proteins associated with fatty acid and glucose metabolism correlate with adaptations in energy expenditure

24-Oct-2015 | Camps, Stefan GJA; Verhoef, Sanne PM; Roumans, Nadia; Bouwman, Freek G; Mariman, Edwin CM; Westerterp, Klaas R, Nutrition & Metabolism, 2015

Background: Energy restriction causes adaptations in energy expenditure (total-,TEE; resting-,REE; activity induced-,AEE).ObjectiveTo determine if changes in the levels of proteins involved in adipocyte glucose and fatty acid metabolism as indicators for energy deficiency are related to ...

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A randomized controlled trial: the effect of inulin on weight management and ectopic fat in subjects with prediabetes

24-Oct-2015 | Guess, Nicola D; Dornhorst, Anne; Oliver, Nick; Bell, Jimmy D; Thomas, E. L; Frost, Gary S, Nutrition & Metabolism, 2015

Background: Fat infiltration of the liver, muscle and pancreas is associated with insulin resistance and risk of diabetes. Weight loss reduces ectopic fat deposition and risk of diabetes, but is difficult to sustain to due to compensatory increases in appetite. Fermentable carbohydrates have been ...

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The origin of β-strand bending in globular proteins

22-Oct-2015 | Fujiwara, Kazuo; Ebisawa, Shinichi; Watanabe, Yuka; Fujiwara, Hiromi; Ikeguchi, Masamichi, BMC Structural Biology, 2015

Background: Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from that for the twist. We, therefore, investigated the physical origin(s) of ...

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Hepatic S1P deficiency lowers plasma cholesterol levels in apoB-containing lipoproteins when LDLR function is compromised

20-Oct-2015 | Basu, Debapriya; Huq, Afroza; Iqbal, Jahangir; Hussain, M. M; Jiang, Xian-Cheng; Jin, Weijun, Nutrition & Metabolism, 2015

Background: Site-1 protease (S1P) is the key enzyme required for activation of the sterol regulatory element binding proteins (SREBPs) that govern lipid synthesis. While S1P has been speculated to influence plasma apoB-containing lipoprotein (Blp) metabolism, there has been little investigative ...

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Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2

09-Oct-2015 | Moreira, Sandrine; Noutahi, Emmanuel; Lamoureux, Guillaume; Burger, Gertraud, BMC Structural Biology, 2015

Background: RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular ...

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