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https://www.readbyqxmd.com/read/28820938/multi-scale-simulation-of-receptor-drug-association-kinetics-application-to-neuramidase-inhibitors
#1
Fabian Zeller, Manuel P Luitz, Rainer Bomblies, Martin Zacharias
A detailed understanding of the drug-receptor association process is of fundamental importance for drug design. Due to the long timescales of typical binding kinetics, the atomistic simulation of the ligand traveling from bulk solution into the binding site is still computationally challenging. In this work, we apply a multi-scale approach of combined molecular dynamics (MD) and Brownian dynamics (BD) simulations to investigate association pathway ensembles for the two prominent H1N1 neuraminidase inhibitors oseltamivir and zanamivir...
August 18, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28820066/mutational-impact-on-the-interaction-between-human-il27-and-gp130-in-silico-approach-for-defending-hiv-infection
#2
Arundhati Banerjee, Rakhi Dasgupta, Sujay Ray
INTRODUCTION: With advances in proteomics, it is essential to investigate the molecular-level participation of IL27 and gp130 to hinder HIV infection. Their interaction causes cell-cycle arrest in HIV+ cells by activating the receptor-associated JAK signaling and causing apoptosis of cancerous cells. METHODOLOGY: The best human wild-type WT_IL27 model was prepared after varied molecular modeling techniques. The vital tyrosine residues in WT_IL27 were identified, mutated and IL27 was re-modeled...
August 17, 2017: Current HIV Research
https://www.readbyqxmd.com/read/28819626/robust-significance-analysis-of-microarrays-by-minimum-%C3%AE-divergence-method
#3
Md Shahjaman, Nishith Kumar, Md Manir Hossain Mollah, Md Shakil Ahmed, Anjuman Ara Begum, S M Shahinul Islam, Md Nurul Haque Mollah
Identification of differentially expressed (DE) genes with two or more conditions is an important task for discovery of few biomarker genes. Significance Analysis of Microarrays (SAM) is a popular statistical approach for identification of DE genes for both small- and large-sample cases. However, it is sensitive to outlying gene expressions and produces low power in presence of outliers. Therefore, in this paper, an attempt is made to robustify the SAM approach using the minimum β-divergence estimators instead of the maximum likelihood estimators of the parameters...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28819254/investigations-of-phase-transformation-in-monocrystalline-silicon-at-low-temperatures-via-nanoindentation
#4
Shunbo Wang, Hang Liu, Lixia Xu, Xiancheng Du, Dan Zhao, Bo Zhu, Miao Yu, Hongwei Zhao
Nanoindentations of monocrystalline silicon are conducted to investigate the phase transformation process at a temperature range from 292 K to 210 K. The load-displacement curves are obtained and the residual indents are detected by Raman spectra. MD simulations are also conducted to identify the phase state during nanoindentation. The results show that the low temperature has no influence on the generation of Si-II during loading process of indentation, but the phenomenon of pop-out is inhibited with the temperature decreasing...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818366/expression-of-recombinant-snrk1-in-e-coli-characterization-of-adenine-nucleotide-binding-to-the-snrk1-1-akin%C3%AE-%C3%AE-%C3%AE-3-complex
#5
José Luis Maya-Bernal, Alejandra Ávila, Ana Ruiz-Gayosso, Ricardo Trejo-Fregoso, Nancy Pulido, Alejandro Sosa-Peinado, Esther Zúñiga-Sánchez, Eleazar Martínez-Barajas, Rogelio Rodríguez-Sotres, Patricia Coello
The SnRK1 complexes in plants belong to the family of AMPK/SNF1 kinases, which have been associated with the control of energy balance, in addition to being involved in the regulation of other aspects of plant growth and development. Analysis of complex formation indicates that increased activity is achieved when the catalytic subunit is phosphorylated and bound to regulatory subunits. SnRK1.1 subunit activity is higher than that of SnRK1.2, which also exhibits reduced activation due to the regulatory subunits...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28818061/estimating-correlation-between-multivariate-longitudinal-data-in-the-presence-of-heterogeneity
#6
Feng Gao, J Philip Miller, Chengjie Xiong, Jingqin Luo, Julia A Beiser, Ling Chen, Mae O Gordon
BACKGROUND: Estimating correlation coefficients among outcomes is one of the most important analytical tasks in epidemiological and clinical research. Availability of multivariate longitudinal data presents a unique opportunity to assess joint evolution of outcomes over time. Bivariate linear mixed model (BLMM) provides a versatile tool with regard to assessing correlation. However, BLMMs often assume that all individuals are drawn from a single homogenous population where the individual trajectories are distributed smoothly around population average...
August 17, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28817081/multiphysics-simulation-of-low-amplitude-acoustic-wave-detection-by-piezoelectric-wafer-active-sensors-validated-by-in-situ-ae-fatigue-experiment
#7
Md Yeasin Bhuiyan, Victor Giurgiutiu
Piezoelectric wafer active sensors (PWAS) are commonly used for detecting Lamb waves for structural health monitoring application. However, in most applications of active sensing, the signals are of high-amplitude and easy to detect. In this article, we have shown a new avenue of using the PWAS transducer for detecting the low-amplitude fatigue-crack related acoustic emission (AE) signals. Multiphysics finite element (FE) simulations were performed with two PWAS transducers bonded to the structure. Various configurations of the sensors were studied by using the simulations...
August 17, 2017: Materials
https://www.readbyqxmd.com/read/28813143/effect-of-structure-and-disorder-on-the-charge-transport-in-defined-self-assembled-monolayers-of-organic-semiconductors
#8
Thomas Schmaltz, Bastian Gothe, Andreas Krause, Susanne Leitherer, Hans-Georg Steinrück, Michael Thoss, Timothy Clark, Marcus Halik
Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising type of organic electronic device but also allow detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-π-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations allows us to characterize self-assembled monolayer (SAM) based devices in great detail...
August 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28813018/biophysical-and-computational-studies-of-the-vcci-vmip-ii-complex
#9
Anna F Nguyen, Nai-Wei Kuo, Laura J Showalter, Ricardo Ramos, Cynthia M Dupureur, Michael E Colvin, Patricia J LiWang
Certain viruses have the ability to subvert the mammalian immune response, including interference in the chemokine system. Poxviruses produce the chemokine binding protein vCCI (viral CC chemokine inhibitor; also called 35K), which tightly binds to CC chemokines. To facilitate the study of vCCI, we first provide a protocol to produce folded vCCI from Escherichia coli (E. coli.) It is shown here that vCCI binds with unusually high affinity to viral Macrophage Inflammatory Protein-II (vMIP-II), a chemokine analog produced by the virus, human herpesvirus 8 (HHV-8)...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28811526/observation-of-the-unexpected-morphology-of-graphene-wrinkle-on-copper-substrate
#10
Wen Wang, Shudu Yang, Ashu Wang
Graphene, a two-dimensional material, has a wide range of unique properties and could be used in the development of varieties of mechanic, electronic and photonic devices, therefore methods to synthesis large-area high-quality graphene films are urgently required. Chemical vapor deposition (CVD) has been of particular interest recently due to its simplicity and low cost. However, because of the mismatch of thermal expansion coefficients, high densities of wrinkles are commonly observed. Despite their prevalence and potential impact on large-scale graphene properties, relatively little is known about their structural morphology and formation mechanism...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811118/prediction-and-characterization-of-the-stability-enhancing-effect-of-the-cherry-tag%C3%A2-in-highly-concentrated-protein-solutions-by-complex-rheological-measurements-and-md-simulations
#11
Pascal Baumann, Marie-Therese Schermeyer, Hannah Burghardt, Cathrin Dürr, Jonas Gärtner, Jürgen Hubbuch
Solution stability attributes are one of the key parameters within the production and launching phase of new biopharmaceuticals. Instabilities of active biological compounds can reduce the yield of biopharmaceutical productions, and may induce undesired reactions in patients, such as immunogenic rejections. Protein solution stability thus needs to be engineered and monitored throughout production and storage. In contrast to the gold standard of long-term storage experiments applied in industry, novel experimental and in silico molecular dynamics tools for predicting protein solution stability can be applied within several minutes or hours...
August 12, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28810783/self-consistent-calculation-of-protein-folding-pathways
#12
S Orioli, S A Beccara, P Faccioli
We introduce an iterative algorithm to efficiently simulate protein folding and other conformational transitions, using state-of-the-art all-atom force fields. Starting from the Langevin equation, we obtain a self-consistent stochastic equation of motion, which directly yields the reaction pathways. From the solution of this set of equations we derive a stochastic estimate of the reaction coordinate. We validate this approach against the results of plain MD simulations of the folding of a small protein, which were performed on the Anton supercomputer...
August 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28809952/computational-and-experimental-analysis-of-short-peptide-motifs-for-enzyme-inhibition
#13
Jinglin Fu, Luca Larini, Anthony J Cooper, John W Whittaker, Azka Ahmed, Junhao Dong, Minyoung Lee, Ting Zhang
The metabolism of living systems involves many enzymes that play key roles as catalysts and are essential to biological function. Searching ligands with the ability to modulate enzyme activities is central to diagnosis and therapeutics. Peptides represent a promising class of potential enzyme modulators due to the large chemical diversity, and well-established methods for library synthesis. Peptides and their derivatives are found to play critical roles in modulating enzymes and mediating cellular uptakes, which are increasingly valuable in therapeutics...
2017: PloS One
https://www.readbyqxmd.com/read/28808266/in-silico-analysis-of-glanzmann-variants-of-calf-1-domain-of-%C3%AE-iib%C3%AE-3-integrin-revealed-dynamic-allosteric-effect
#14
Matthieu Goguet, Tarun Jairaj Narwani, Rachel Petermann, Vincent Jallu, Alexandre G de Brevern
Integrin αIIbβ3 mediates platelet aggregation and thrombus formation. In a rare hereditary bleeding disorder, Glanzmann thrombasthenia (GT), αIIbβ3 expression / function are impaired. The impact of deleterious missense mutations on the complex structure remains unclear. Long independent molecular dynamics (MD) simulations were performed for 7 GT variants and reference structure of the Calf-1 domain of αIIb. Simulations were analysed using a structural alphabet to describe local protein conformations. Common and flexible regions as well as deformable zones were observed in all the structures...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807997/phosphoantigen-induced-conformational-change-of-butyrophilin-3a1-btn3a1-and-its-implication-on-v%C3%AE-9v%C3%AE-2-t-cell-activation
#15
Siyi Gu, Joseph R Sachleben, Christopher T Boughter, Wioletta I Nawrocka, Marta T Borowska, Jeffrey T Tarrasch, Georgios Skiniotis, Benoît Roux, Erin J Adams
Human Vγ9Vδ2 T cells respond to microbial infections as well as certain types of tumors. The key initiators of Vγ9Vδ2 activation are small, pyrophosphate-containing molecules called phosphoantigens (pAgs) that are present in infected cells or accumulate intracellularly in certain tumor cells. Recent studies demonstrate that initiation of the Vγ9Vδ2 T cell response begins with sensing of pAg via the intracellular domain of the butyrophilin 3A1 (BTN3A1) molecule. However, it is unknown how downstream events can ultimately lead to T cell activation...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28805390/sampling-long-versus-short-range-interactions-defines-the-ability-of-force-fields-to-reproduce-the-dynamics-of-intrinsically-disordered-proteins
#16
Davide Mercadante, Johannes Andreas Wagner, Iker Valle Aramburu, Edward A Lemke, Frauke Gräter
Molecular dynamics simulations have valuably complemented experiments describing the dynamics of intrinsically disordered proteins (IDPs), particularly since the proposal of models to solve the artificial collapse of IDPs in silico. Such models suggest redefining non-bonded interactions, by either increasing water dispersion forces or adopting the Kirkwood-Buff force field. These approaches yield extended conformers that better comply with experiments, but it is unclear if they all sample the same intra-chain dynamics of IDPs...
August 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28805377/intrinsic-dynamics-of-binding-rail-and-its-allosteric-effect-in-the-class-i-hdacs
#17
Jingwei Zhou, Yue Huang, Chunyan Cheng, Kai Wang, Ruibo Wu
The development of novel isoform/class-selective inhibitor is still of great biological and medical significance to conquer the continuously reported side effects for the histone deacetylases (HDACs) drugs. The first potent HDAC allosteric inhibitor was discovered last year and this allosteric inhibitor design is thought to be a promising strategy to overcome the current challenges in HDAC inhibitor design. However, the detailed allosteric mechanisms and its remote regulation effects on the catalytic/inhibitor activity of HDAC are still unclear...
August 14, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28805211/all-atom-md-indicates-ion-dependent-behavior-of-therapeutic-dna-polymer
#18
Ryan L Melvin, William H Gmeiner, Freddie R Salsbury
Understanding the efficacy of and creating delivery mechanisms for therapeutic nucleic acids requires understanding structural and kinetic properties which allow these polymers to promote the death of cancerous cells. One molecule of interest is a 10 mer of FdUMP (5-fluoro-2'-deoxyuridine-5'-O-monophosphate) - also called F10. Here we investigate the structural and kinetic behavior of F10 in intracellular and extracellular solvent conditions along with non-biological conditions that may be efficacious in in vitro preparations of F10 delivery systems...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28805144/a-qm-protein-ligand-investigation-of-anti-psychotic-drugs-with-the-dopamine-d2-receptor-d2r
#19
Ramin Ekhteiari Salmas, Yusuf Serhat Is, Serdar Durdagi, Matthias Stein, Mine Yurtsever
The dopamine D2 Receptor (D2R) is a member of the G-Protein Coupled Receptor (GPCR) family and plays a critical role in neurotransmission activities in the human brain. Dysfunction in dopamine receptor signaling may lead to mental health illnesses such as schizophrenia and Parkinson's disease. D2R is the target protein of the commonly used anti-psychotic drugs such as risperidone, clozapine, aripiprazole, olanzapine, ziprasidone and quetiapine. Due to their significant side effects and nonselective profiles, the discovery of novel drugs has become a challenge for researchers working in this field...
August 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28803469/chiral-ceramic-nanoparticles-of-tungsten-oxide-and-peptide-catalysis
#20
Shuang Jiang, Mahshid Chekini, Zhi-Bei Qu, Yichun Wang, Aydan Yeltik, Yuangang Liu, Alex Kotlyar, Tianyong Zhang, Bin Li, Hilmi Volkan Demir, Nicholas A Kotov
The chirality of nanoparticles (NPs) and their assemblies has been investigated predominantly for noble metals and II-VI semiconductors. However, ceramic NPs represent the majority of nanoscale materials in Nature. The robustness and other innate properties of ceramics offer technological opportunities in catalysis, biomedical sciences, and optics. Here we report the preparation of chiral ceramic NPs, as represented by tungsten oxide hydrate, WO3-x·H2O, dispersed in ethanol. The chirality of the metal oxide core, with an average size of ca 1...
August 12, 2017: Journal of the American Chemical Society
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