Search Results - "Wassenaar, A"

Backmapping triangulated surfaces to coarse-grained membrane models by Pezeshkian, Weria, König, Melanie, Wassenaar, Tsjerk A., Marrink, Siewert J.

“…Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide…”
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Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models by Wassenaar, Tsjerk A, Pluhackova, Kristyna, Böckmann, Rainer A, Marrink, Siewert J, Tieleman, D. Peter

“…The conversion of coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations…”
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Improved Parameters for the Martini Coarse-Grained Protein Force Field by de Jong, Djurre H, Singh, Gurpreet, Bennett, W. F. Drew, Arnarez, Clement, Wassenaar, Tsjerk A, Schäfer, Lars V, Periole, Xavier, Tieleman, D. Peter, Marrink, Siewert J

“…The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)­molecular systems. Recent progress in our ability to…”
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Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4 by Pluhackova, Kristyna, Gahbauer, Stefan, Kranz, Franziska, Wassenaar, Tsjerk A, Böckmann, Rainer A

“…G protein coupled receptors (GPCRs) allow for the transmission of signals across biological membranes. For a number of GPCRs, this signaling was shown to be…”
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LION/web: a web-based ontology enrichment tool for lipidomic data analysis by Molenaar, Martijn R, Jeucken, Aike, Wassenaar, Tsjerk A, van de Lest, Chris H A, Brouwers, Jos F, Helms, J Bernd

“…Abstract Background A major challenge for lipidomic analyses is the handling of the large amounts of data and the translation of results to interpret the…”
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Relationship Between CYP2A6 and CHRNA5-CHRNA3-CHRNB4 Variation and Smoking Behaviors and Lung Cancer Risk by Wassenaar, Catherine A., Dong, Qiong, Wei, Qingyi, Amos, Christopher I., Spitz, Margaret R., Tyndale, Rachel F.

“…Genetic variations in the CYP2A6 nicotine metabolic gene and the CHRNA5-CHRNA3-CHRNB4 (CHRNA5-A3-B4) nicotinic gene cluster have been independently associated…”
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Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins by Corradi, Valentina, Mendez-Villuendas, Eduardo, Ingólfsson, Helgi I, Gu, Ruo-Xu, Siuda, Iwona, Melo, Manuel N, Moussatova, Anastassiia, DeGagné, Lucien J, Sejdiu, Besian I, Singh, Gurpreet, Wassenaar, Tsjerk A, Delgado Magnero, Karelia, Marrink, Siewert J, Tieleman, D. Peter

“…Cell membranes contain hundreds of different proteins and lipids in an asymmetric arrangement. Our current understanding of the detailed organization of cell…”
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Multinational development and validation of an early prediction model for delirium in ICU patients by Wassenaar, A., van den Boogaard, M., van Achterberg, T., Slooter, A. J. C., Kuiper, M. A., Hoogendoorn, M. E., Simons, K. S., Maseda, E., Pinto, N., Jones, C., Luetz, A., Schandl, A., Verbrugghe, W., Aitken, L. M., van Haren, F. M. P., Donders, A. R. T., Schoonhoven, L., Pickkers, P.

“…Rationale Delirium incidence in intensive care unit (ICU) patients is high and associated with poor outcome. Identification of high-risk patients may…”
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Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness by Cybulski, Larisa Estefanía, Ballering, Joost, Moussatova, Anastassiia, Inda, Maria Eugenia, Vazquez, Daniela B., Wassenaar, Tsjerk A., de Mendoza, Diego, Tieleman, D. Peter, Killian, J. Antoinette

“…DesK is a bacterial thermosensor protein involved in maintaining membrane fluidity in response to changes in environmental temperature. Most likely, the…”
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Martini 3: a general purpose force field for coarse-grained molecular dynamics by Souza, Paulo C. T., Alessandri, Riccardo, Barnoud, Jonathan, Thallmair, Sebastian, Faustino, Ignacio, Grünewald, Fabian, Patmanidis, Ilias, Abdizadeh, Haleh, Bruininks, Bart M. H., Wassenaar, Tsjerk A., Kroon, Peter C., Melcr, Josef, Nieto, Vincent, Corradi, Valentina, Khan, Hanif M., Domański, Jan, Javanainen, Matti, Martinez-Seara, Hector, Reuter, Nathalie, Best, Robert B., Vattulainen, Ilpo, Monticelli, Luca, Periole, Xavier, Tieleman, D. Peter, de Vries, Alex H., Marrink, Siewert J.

“…The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with…”
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Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain by Jayaraman, Kumaresan, Morley, Alex N, Szöllősi, Daniel, Wassenaar, Tsjerk A, Sitte, Harald H, Stockner, Thomas

“…The human dopamine transporter (hDAT) is located on presynaptic neurons, where it plays an essential role in limiting dopaminergic signaling by temporarily…”
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CYP2A6 reduced activity gene variants confer reduction in lung cancer risk in African American smokers--findings from two independent populations by Wassenaar, Catherine A, Ye, Yuanqing, Cai, Qiuyin, Aldrich, Melinda C, Knight, Joanne, Spitz, Margaret R, Wu, Xifeng, Blot, William J, Tyndale, Rachel F

“…We investigated genetic variation in CYP2A6 in relation to lung cancer risk among African American smokers, a high-risk population. Previously, we found that…”
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Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations by Han, Jing, Pluhackova, Kristyna, Wassenaar, Tsjerk A., Böckmann, Rainer A.

“…Synaptic vesicle fusion requires assembly of the SNARE complex composed of SNAP-25, syntaxin-1, and synaptobrevin-2 (sybII) proteins. The SNARE proteins found…”
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Structural Aspects of the ROS1 Kinase Domain and Oncogenic Mutations by Vilachã, Juliana F, Wassenaar, Tsjerk A, Marrink, Siewert J

“…Protein kinases function as pivotal regulators in biological events, governing essential cellular processes through the transfer of phosphate groups from ATP…”
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Thermodynamic and kinetic characterization of transmembrane helix association by Pawar, Aiswarya B, Deshpande, Sneha A, Gopal, Srinivasa M, Wassenaar, Tsjerk A, Athale, Chaitanya A, Sengupta, Durba

“…The transient dimerization of transmembrane proteins is an important event in several cellular processes and computational methods are being increasingly used…”
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Constraint-Induced Movement Therapy Results in Increased Motor Map Area in Subjects 3 to 9 Months After Stroke by Sawaki, Lumy, Butler, Andrew J., Xiaoyan Leng, Wassenaar, Peter A., Mohammad, Yousef M., Blanton, Sarah, Sathian, K., Nichols-Larsen, Deborah S., Wolf, Steven L., Good, David C., Wittenberg, George F.

“…Background. Constraint-induced movement therapy (CIMT) has received considerable attention as an intervention to enhance motor recovery and cortical…”
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Standard lymph node dissection for bladder cancer: significant variability in the number of reported lymph nodes by Meijer, R P, Meijer, R P P, Nunnink, C J M, Wassenaar, A E, Bex, A, van der Poel, H G, van Rhijn, B W, Meinhardt, W, Horenblas, S

“…We compared the nodal yield after histopathological examination of extended bilateral pelvic lymph node dissection specimens for bladder cancer at 2 hospitals…”
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Differential patterns of cortical reorganization following constraint-induced movement therapy during early and late period after stroke: A preliminary study by Sawaki, Lumy, Butler, Andrew J, Leng, Xiaoyan, Wassenaar, Peter A, Mohammad, Yousef M, Blanton, Sarah, Sathian, K, Nichols-Larsen, Deborah S, Wolf, Steven L, Good, David C, Wittenberg, George F

“…Constraint-induced movement therapy (CIMT) has been shown to improve upper extremity voluntary movement and change cortical movement representation after…”
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Competing Roles of Ca2+ and Nonmuscle Myosin IIA on the Dynamics of the Metastasis-Associated Protein S100A4 by Yildirim, Ahmet, Tekpinar, Mustafa, Wassenaar, Tsjerk A

“…The calcium-binding protein S100A4 plays an important role in a wide range of biological processes such as cell motility, invasion, angiogenesis, survival,…”
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Competing Roles of Ca 2+ and Nonmuscle Myosin IIA on the Dynamics of the Metastasis-Associated Protein S100A4 by Yildirim, Ahmet, Tekpinar, Mustafa, Wassenaar, Tsjerk A

“…The calcium-binding protein S100A4 plays an important role in a wide range of biological processes such as cell motility, invasion, angiogenesis, survival,…”
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