Search Results - "Yao, Xin‐Qiu"

The Bio3D packages for structural bioinformatics by Grant, Barry J., Skjærven, Lars, Yao, Xin‐Qiu

“…Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database…”
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Tuning Protein Dynamics to Sense Rapid Endoplasmic‐Reticulum Calcium Dynamics by Deng, Xiaonan, Yao, Xin‐Qiu, Berglund, Ken, Dong, Bin, Ouedraogo, Daniel, Ghane, Mohammad A., Zhuo, You, McBean, Cheyenne, Wei, Zheng Zachory, Gozem, Samer, Yu, Shan P., Wei, Ling, Fang, Ning, Mabb, Angela M., Gadda, Giovanni, Hamelberg, Donald, Yang, Jenny J.

“…Multi‐scale calcium (Ca2+) dynamics, exhibiting wide‐ranging temporal kinetics, constitutes a ubiquitous mode of signal transduction. We report a novel…”
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Comparative structural dynamic analysis of GTPases by Li, Hongyang, Yao, Xin-Qiu, Grant, Barry J

“…GTPases regulate a multitude of essential cellular processes ranging from movement and division to differentiation and neuronal activity. These ubiquitous…”
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Dissecting the Allosteric Fine-Tuning of Enzyme Catalysis by Yao, Xin-Qiu, Hamelberg, Donald

“…Fully understanding the mechanism of allosteric regulation in biomolecules requires separating and examining all of the involved factors. In enzyme catalysis,…”
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Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells by Stender, Joshua D., Nwachukwu, Jerome C., Kastrati, Irida, Kim, Yohan, Strid, Tobias, Yakir, Maayan, Srinivasan, Sathish, Nowak, Jason, Izard, Tina, Rangarajan, Erumbi S., Carlson, Kathryn E., Katzenellenbogen, John A., Yao, Xin-Qiu, Grant, Barry J., Leong, Hon S., Lin, Chin-Yo, Frasor, Jonna, Nettles, Kendall W., Glass, Christopher K.

“…Human breast cancers that exhibit high proportions of immune cells and elevated levels of pro-inflammatory cytokines predict poor prognosis. Here, we…”
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CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work by Kenzaki, Hiroo, Koga, Nobuyasu, Hori, Naoto, Kanada, Ryo, Li, Wenfei, Okazaki, Kei-ichi, Yao, Xin-Qiu, Takada, Shoji

“…For simulating proteins at work in millisecond time scale or longer, we develop a coarse-grained (CG) molecular dynamics (MD) method and software, CafeMol. At…”
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Drug Uptake Pathways of Multidrug Transporter AcrB Studied by Molecular Simulations and Site-Directed Mutagenesis Experiments by Yao, Xin-Qiu, Kimura, Nobuhiro, Murakami, Satoshi, Takada, Shoji

“…Multidrug resistance has been a critical issue in current chemotherapy. In Escherichia coli, a major efflux pump responsible for the multidrug resistance…”
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Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations by Takada, Shoji, Yao, Xin-Qiu, Kenzaki, Hiroo, Murakami, Satoshi

“…Multidrug resistance is a serious problem in current chemotherapy. The efflux system largely responsible for resistance in Escherichia coli contains the drug…”
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Piperlongumine induces apoptotic and autophagic death of the primary myeloid leukemia cells from patients via activation of ROS-p38/JNK pathways by Xiong, Xin-xin, Liu, Ju-mei, Qiu, Xin-yao, Pan, Feng, Yu, Shang-bin, Chen, Xiao-qian

“…Aim： To investigate the effects of piperlongumine （PL）, an anticancer alkaloid from long pepper plants, on the primary myeloid leukemia cells from patients and…”
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Structural Determinants Influencing the Potency and Selectivity of Indazole-Paroxetine Hybrid G Protein-Coupled Receptor Kinase 2 Inhibitors by Bouley, Renee, Waldschmidt, Helen V, Cato, M Claire, Cannavo, Alessandro, Song, Jianliang, Cheung, Joseph Y, Yao, Xin-Qiu, Koch, Walter J, Larsen, Scott D, Tesmer, John J G

“…G protein-coupled receptor kinases (GRKs) phosphorylate activated receptors to promote arrestin binding, decoupling from heterotrimeric G proteins, and…”
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A dynamic Bayesian network approach to protein secondary structure prediction by Yao, Xin-Qiu, Zhu, Huaiqiu, She, Zhen-Su

“…Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful…”
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Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins by Ahmed, Furyal, Yao, Xin-Qiu, Hamelberg, Donald

“…Cyclophilins are ubiquitous human enzymes that catalyze peptidyl-prolyl cis–trans isomerization in protein substrates. Of the 17 unique isoforms, five closely…”
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Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis by Yao, Xin-Qiu, Momin, Mohamed, Hamelberg, Donald

“…A difference contact network analysis (dCNA) method is developed for delineating allosteric mechanisms in proteins. The new method addresses limitations of…”
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Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis by Yao, Xin-Qiu, Hamelberg, Donald

“…Conspectus Recent advances have made all-atom molecular dynamics (MD) a powerful tool to sample the conformational energy landscape. There are still however…”
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Evolving Mutational Buildup in HIV‑1 Protease Shifts Conformational Dynamics to Gain Drug Resistance by Souffrant, Michael, Yao, Xin-Qiu, Hamelberg, Donald

“…Drug resistance in antiviral treatments is a serious public health problem. Viral proteins mutate very fast, giving them a way to escape drugs by lowering drug…”
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Integrating protein structural dynamics and evolutionary analysis with Bio3D by Skjærven, Lars, Yao, Xin-Qiu, Scarabelli, Guido, Grant, Barry J

“…Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations…”
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p53 Is Potentially Regulated by Cyclophilin D in the Triple-Proline Loop of the DNA Binding Domain by Kumutima, Jacques, Yao, Xin-Qiu, Hamelberg, Donald

“…The multifunctional protein p53 is the central molecular sensor of cellular stresses. The canonical function of p53 is to transcriptionally activate target…”
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Residue–Residue Contact Changes during Functional Processes Define Allosteric Communication Pathways by Yao, Xin-Qiu, Hamelberg, Donald

“…Allosteric regulation plays a central role in orchestrating diverse cellular processes. A prerequisite for allostery is a flexible biomolecule within which two…”
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Advances in Hypoxia-Mediated Mechanisms in Hepatocellular Carcinoma by Xiong, Xin Xin, Qiu, Xin Yao, Hu, Dian Xing, Chen, Xiao Qian

“…Hepatocellular carcinoma (HCC) is the fifth most common and the third most deadly malignant tumor worldwide. Hypoxia and related oxidative stress are heavily…”
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Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d‑Arginine Dehydrogenase by Ouedraogo, Daniel, Souffrant, Michael, Yao, Xin-Qiu, Hamelberg, Donald, Gadda, Giovanni

“…Numerous studies demonstrate that enzymes undergo multiple conformational changes during catalysis. The malleability of enzymes forms the basis for allosteric…”
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