Search Results - "Ido, Y."

Simulating Water Exchange to Buried Binding Sites by Ben-Shalom, Ido Y, Lin, Charles, Kurtzman, Tom, Walker, Ross C, Gilson, Michael K

“…Traditional molecular dynamics (MD) simulations of proteins, which relies on integration of Newton’s equations of motion, cannot efficiently equilibrate water…”
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Accounting for the Central Role of Interfacial Water in Protein–Ligand Binding Free Energy Calculations by Ben-Shalom, Ido Y, Lin, Zhixiong, Radak, Brian K, Lin, Charles, Sherman, Woody, Gilson, Michael K

“…Rigorous binding free energy methods in drug discovery are growing in popularity because of a combination of methodological advances, improvements in computer…”
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Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations by Ben-Shalom, Ido Y, Pfeiffer-Marek, Stefania, Baringhaus, Karl-Heinz, Gohlke, Holger

“…A major uncertainty in binding free energy estimates for protein–ligand complexes by methods such as MM-PB­(GB)­SA or docking scores results from neglecting or…”
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Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units by Ben-Shalom, Ido Y, Lin, Charles, Radak, Brian K, Sherman, Woody, Gilson, Michael K

“…Molecular dynamics (MD) simulations of proteins are commonly used to sample from the Boltzmann distribution of conformational states, with wide-ranging…”
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Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo by Bergazin, Teresa Danielle, Ben-Shalom, Ido Y., Lim, Nathan M., Gill, Sam C., Gilson, Michael K., Mobley, David L.

“…Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can…”
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Native metabolomics identifies the rivulariapeptolide family of protease inhibitors by Reher, Raphael, Aron, Allegra T., Fajtová, Pavla, Stincone, Paolo, Wagner, Berenike, Pérez-Lorente, Alicia I., Liu, Chenxi, Shalom, Ido Y. Ben, Bittremieux, Wout, Wang, Mingxun, Jeong, Kyowon, Matos-Hernandez, Marie L., Alexander, Kelsey L., Caro-Diaz, Eduardo J., Naman, C. Benjamin, Scanlan, J. H. William, Hochban, Phil M. M., Diederich, Wibke E., Molina-Santiago, Carlos, Romero, Diego, Selim, Khaled A., Sass, Peter, Brötz-Oesterhelt, Heike, Hughes, Chambers C., Dorrestein, Pieter C., O’Donoghue, Anthony J., Gerwick, William H., Petras, Daniel

“…The identity and biological activity of most metabolites still remain unknown. A bottleneck in the exploration of metabolite structures and pharmaceutical…”
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Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules by Gohlke, Holger, Ben-Shalom, Ido Y, Kopitz, Hannes, Pfeiffer-Marek, Stefania, Baringhaus, Karl-Heinz

“…We introduce a computationally efficient approximation of vibrational entropy changes (ΔS vib) upon binding to biomolecules based on rigidity theory. From…”
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Measurement of thermal influence on a two-dimensional motion trajectory using a tracking interferometer by Ibaraki, S., Blaser, P., Shimoike, M., Takayama, N., Nakaminami, M., Ido, Y.

“…Conventional thermal deformation tests in ISO 230-3:2007 only measure the tool displacement when it is positioned at a single point. This paper proposes the…”
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Inactivation of AMPK alters gene expression and promotes growth of prostate cancer cells by Zhou, J, Huang, W, Tao, R, Ibaragi, S, Lan, F, Ido, Y, Wu, X, Alekseyev, Y O, Lenburg, M E, Hu, G-f, Luo, Z

“…AMP-activated protein kinase (AMPK) serves as a fuel-sensing enzyme that is activated by binding of AMP and subsequent phophorylation by upstream kinases such…”
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Hypothalamic ATF3 is involved in regulating glucose and energy metabolism in mice by Lee, Y.-S., Sasaki, T., Kobayashi, M., Kikuchi, O., Kim, H.-J., Yokota-Hashimoto, H., Shimpuku, M., Susanti, V.-Y., Ido-Kitamura, Y., Kimura, K., Inoue, H., Tanaka-Okamoto, M., Ishizaki, H., Miyoshi, J., Ohya, S., Tanaka, Y., Kitajima, S., Kitamura, T.

“…Aims/hypothesis The pancreas and hypothalamus are critical for maintaining nutrient and energy homeostasis, and combined disorders in these organs account for…”
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Design optimization and development of CNC lathe headstock to minimize thermal deformation by Mori, M., Mizuguchi, H., Fujishima, M., Ido, Y., Mingkai, N., Konishi, K.

“…This paper has investigated an approach to reduce and compensate thermal displacement for high accuracy NC lathes. An efficient design and optimization method…”
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Microdisk lasers and field effect transistors of thiophene/phenylene co-oligomers by using high temperature deposition method by Sasaki, F., Mori, M., Haraichi, S., Ido, Y., Masumoto, Y., Hotta, S.

“…Microdisk lasers of the organic semiconductor material thiophene/phenylene co-oligomer (TPCO) have been fabricated on Si/SiO 2 substrates. Quality of the…”
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Distribution of micrometer-size particles in magnetic fluids in the presence of steady uniform magnetic field by Ido, Y., Yamaguchi, T., Kiuchi, Y.

“…In this paper, distribution of suspended micrometer-size particles in magnetic fluids is investigated. Microstructure formation of particles in magnetic fluids…”
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Prevention of Vascular and Neural Dysfunction in Diabetic Rats by C-Peptide by Ido, Y., Vindigni, A., Chang, K., Stramm, L., Chance, R., Heath, W. F., DiMarchi, R. D., Di Cera, E., Williamson, J. R.

“…C-peptide, a cleavage product from the processing of proinsulin to insulin, has been considered to possess little if any biological activity other than its…”
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Wideband Planar Folded Dipole Antenna With Self-balanced Impedance Property by Tanaka, S., Yongho Kim, Morishita, H., Horiuchi, S., Atsumi, Y., Ido, Y.

“…A planar folded dipole antenna that exhibits wideband characteristics is proposed. The antenna has simple planar construction without a ground plane and is…”
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Aminoguanidine, a novel inhibitor of nitric oxide formation, prevents diabetic vascular dysfunction by J A Corbett, R G Tilton, K Chang, K S Hasan, Y Ido, J L Wang, M A Sweetland, J R Lancaster, Jr, J R Williamson, M L McDaniel

“…Aminoguanidine, a novel inhibitor of nitric oxide formation, prevents diabetic vascular dysfunction. J A Corbett , R G Tilton , K Chang , K S Hasan , Y Ido , J…”
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Malonyl-CoA and AMP-activated protein kinase (AMPK): possible links between insulin resistance in muscle and early endothelial cell damage in diabetes by Ruderman, N B, Cacicedo, J M, Itani, S, Yagihashi, N, Saha, A K, Ye, J M, Chen, K, Zou, M, Carling, D, Boden, G, Cohen, R A, Keaney, J, Kraegen, E W, Ido, Y

“…Based on available evidence, we would propose the following. (i) Excesses of glucose and free fatty acids cause insulin resistance in skeletal muscle and…”
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Cytosolic NADH/NAD+, free radicals, and vascular dysfunction in early diabetes mellitus by Ido, Y, Kilo, C, Williamson, J R

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Inhibition of sorbitol dehydrogenase. Effects on vascular and neural dysfunction in streptozocin-induced diabetic rats by Tilton, R. G., Chang, K., Nyengaard, J. R., Van den Enden, M., Ido, Y., Williamson, J. R.

“…Inhibition of sorbitol dehydrogenase. Effects on vascular and neural dysfunction in streptozocin-induced diabetic rats. R G Tilton , K Chang , J R Nyengaard ,…”
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Vascular dysfunction induced by elevated glucose levels in rats is mediated by vascular endothelial growth factor by Tilton, R G, Kawamura, T, Chang, K C, Ido, Y, Bjercke, R J, Stephan, C C, Brock, T A, Williamson, J R

“…The purpose of these experiments was to investigate a potential role for vascular endothelial growth factor (VEGF) in mediating vascular dysfunction induced by…”
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