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dimkas simulation [36 articles]

Neue Publikationen in dimkas Bibliothek eingetragen unter dem Bezeichner: simulation. You can also see everyone's simulation.
  • Molecular dynamics simulation of hydrated phospholipid bilayers.
    Indian journal of biochemistry & biophysics, Vol. 33, No. 6. (December 1996), pp. 431-447.
    by V Kothekar
    posted to simulation membrane md lipid dmpc by dimka on 2008-08-20 19:33:30 as **
  • Cholesterol Packing around Lipids with Saturated and Unsaturated Chains: A Simulation Study
    Langmuir (3 June 2008)
    by Sagar A Pandit, See-Wing Chiu, Eric Jakobsson, Ananth Grama, HL Scott
    posted to simulation md dopc cholesterol by dimka on 2008-08-18 22:53:18 as ** along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
  • Effective Mast Cell Degranulating Peptide Inhibitors of the IgE/FcepsilonRI Receptor Interaction.
    Chemical biology & drug design (3 July 2008)
    by Angeliki Buku, Inna Keselman, Dmitry Lupyan, Mihaly Mezei, Joseph A A Price
    posted to simulation peptide md mcd ige-receptor ige by dimka on 2008-07-29 21:44:13 as ** along with 1 person yanz
  • Mechanism of Na+/H+ Antiporting
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 799-803.
    by Isaiah T Arkin, Huafeng Xu, Morten O Jensen, Eyal Arbely, Estelle R Bennett, Kevin J Bowers, Edmond Chow, Ron O Dror, Michael P Eastwood, Ravenna Flitman-Tene, Brent A Gregersen, John L Klepeis, Istvan Kolossvary, Yibing Shan, David E Shaw
    posted to simulation membrane md desmond by dimka on 2008-07-08 21:34:50 as ** along with 4 people and 1 group sobolevnrm Jporci MMehrotra LamBras baker-group
  • Conformational Changes and Gating at the Selectivity Filter of Potassium Channels
    J. Am. Chem. Soc. (28 June 2008)
    by Carmen Domene, Michael L Klein, Davide Branduardi, Francesco L Gervasio, Michele Parrinello
    posted to simulation selectivity md lipids kirbac by dimka on 2008-07-01 00:10:09 as **
  • Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers
    European Biophysics Journal, Vol. 37, No. 2. (11 February 2008), pp. 131-141.
    by Katherine Cox, Peter Bond, Alessandro Grottesi, Marc Baaden, Mark Sansom
    posted to simulation protein membrane md compare by dimka on 2008-06-25 16:48:52 as **
  • Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study
    Biophys. J., Vol. 88, No. 6. (1 June 2005), pp. 3822-3828.
    by Steve O Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B Moore, Michael L Klein
    posted to simulation perturbation nanotube md lipid by dimka on 2008-05-13 21:14:16 as ** along with 1 person loison
  • Focus on Kir6.2: a key component of the ATP-sensitive potassium channel.
    Journal of molecular and cellular cardiology, Vol. 38, No. 6. (June 2005), pp. 927-936.
    by S Haider, JF Antcliff, P Proks, MS Sansom, FM Ashcroft
    posted to simulation md kir62 katp atp by dimka on 2008-05-09 21:33:30 as **
  • Homology Modeling and Molecular Dynamics Simulation Studies of an Inward Rectifier Potassium Channel
    Biophys. J., Vol. 78, No. 6. (1 June 2000), pp. 2929-2942.
    by Charlotte E Capener, Indira H Shrivastava, Kishani M Ranatunga, Lucy R Forrest, Graham R Smith, Mark S Sansom
    posted to tertiapin simulation kir kcsa by dimka on 2008-05-09 20:40:16 as **
  • Effect of Ions on a Dipalmitoyl Phosphatidylcholine Bilayer. A Molecular Dynamics Simulation Study
    J. Phys. Chem. B (15 January 2008)
    by A Cordomi, O Edholm, JJ Perez
    posted to simulation lipid-area lipid dppc by dimka on 2008-05-08 23:58:41 as ** along with 2 people and 1 group sobolevnrm softsimu baker-group
  • Molecular dynamics simulations of potassium channels
    Central European Journal of Chemistry, Vol. 5, No. 3. (2007), pp. 635-671.
    by Carmen Domene
    posted to simulation review md kir channels by dimka on 2008-05-08 23:28:34 as **
  • Biological Membranes: A Molecular Perspective from Computation and Experiment
    (30 July 1996)
    by Kenneth Merz, Benoit Roux
    posted to simulation membrane lipid by dimka on 2008-05-07 07:29:15 as **
  • Electrostatic contribution to the surface pressure of charged monolayers containing polyphosphoinositides
    Biophys. J. (25 April 2008), biophysj.107.126615.
    by Ilya Levental, Paul A Janmey, Andrejs Cebers
    posted to simulation pip2 pi calculation by dimka on 2008-04-29 20:33:09 as ** along with 1 person paulschlesinger
  • The Role of Conformation in Ion Permeation in a K+ Channel
    J. Am. Chem. Soc. (23 February 2008)
    by C Domene, S Vemparala, S Furini, K Sharp, ML Klein
    posted to kirbac11 lipid md permeation simulation by dimka on 2008-02-25 00:44:04 as **
  • Dynamic Relationships among Type IIa Bacteriocins: Temperature Effects on Antimicrobial Activity and on Structure of the C-Terminal Amphipathic Alpha-Helix as a Receptor-Binding Region
    Biochemistry, Vol. 43, No. 28. (20 July 2004), pp. 9009-9020.
    by K Kaur, LC Andrew, DS Wishart, JC Vederas
    posted to folding md peptide simulation by dimka on 2007-11-20 20:30:34 as **
  • Electrostatic interactions in phospholipid membranes revealed by coherent 2D IR spectroscopy
    Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15323-15327.
    by VV Volkov, R Chelli, W Zhuang, F Nuti, Y Takaoka, AM Papini, S Mukamel, R Righini
    posted to dmpc experimental lipid md membrane simulation by dimka on 2007-10-31 15:52:35 as ** along with 1 person and 1 group sobolevnrm baker-group
  • A consensus view of protein dynamics.
    Proc Natl Acad Sci U S A (10 January 2007)
    by Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluis L Gelpí, Modesto Orozco
    posted to benchmark md simulation by dimka on 2007-02-19 23:50:00 as ** along with 12 people and 2 groups LamBras lna aqeel aswin rabio grahamc hmk zwang biehl Ema phoenixzxl ras ParkinsonLab_at_MaRS The BMM Dome
  • Ion Conduction through MscS as Determined by Electrophysiology and Simulation.
    Biophys J (17 November 2006)
    by Marcos Sotomayor, Valeria Vasquez, Eduardo Perozo, Klaus Schulten
    posted to channel lipid membrane mscs simulation by dimka on 2006-11-28 20:25:33 as *****
  • Investigation of finite system-size effects in molecular dynamics simulations of lipid bilayers.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 47. (30 November 2006), pp. 24157-24164.
    by F Castro-Roman, RW Benz, SH White, DJ Tobias
    posted to dopc lipid simulation by dimka on 2006-11-28 20:18:25 as **
  • Effect of Cholesterol on the Properties of Phospholipid Membranes. 4. Interatomic Voids.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 109, No. 34. (1 September 2005), pp. 16490-16502.
    by Marina G Alinchenko, Vladimir P Voloshin, Nikolai N Medvedev, Mihaly Mezei, Lívia Partay, Pal Jedlovszky
    posted to cholesterol dmpc dynamic lipids md membrane simulation by dimka on 2006-07-27 21:25:14 as **
  • Molecular Dynamics study of MscL interactions with a curved lipid bilayer.
    Biophys J (2 June 2006)
    by Grischa R R Meyer, Justin Gullingsrud, Klaus Schulten, Boris Martinac
    posted to lipids md mechanosensitive membrane mscl simulation by dimka on 2006-06-09 18:38:04 as ***
  • Model for the structure of the lipid bilayer.
    Proc Natl Acad Sci U S A, Vol. 88, No. 3. (1 February 1991), pp. 892-896.
    by RW Pastor, RM Venable, M Karplus
    posted to membrane simulation by dimka on 2006-06-09 18:32:25 as **
  • An Energy-Efficient Gating Mechanism in the Acetylcholine Receptor Channel Suggested by Molecular and Brownian Dynamics
    Biophys. J., Vol. 90, No. 3. (1 February 2006), pp. 799-810.
    by Ben Corry
    posted to ach-receptor-channel bd brownian channel dynamics gating simulation by dimka on 2006-05-20 21:44:28 as **
  • MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
    Protein Sci, Vol. 11, No. 11. (1 November 2002), pp. 2606-2621.
    by Angel R Ortiz, Charlie E Strauss, Osvaldo Olmea
    posted to algorithm alignment conformation databases folding mammoth models molecular protein secondary simulation software statistics structure by dimka on 2006-03-28 23:52:07 as read along with 6 people and 2 groups tjimenez sebk ana iakes jwm analogAI structural_bioinformatics Bioinformatics
  • A molecular dynamics study of an archaeal tetraether lipid membrane: comparison with a dipalmitoylphosphatidylcholine lipid bilayer.
    Lipids, Vol. 40, No. 10. (October 2005), pp. 1023-1030.
    by JP Nicolas
    posted to dppc membrane simulation by dimka on 2006-03-06 16:16:42 as **
  • BioShella package of tools for structural biology computations
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 621-622.
    by Dominik Gront, Andrzej Kolinski
    posted to analysis md simulation tool trajectory by dimka on 2006-03-01 18:47:39 as ** along with 5 people bicko chad_davis dgront rabio mijam
  • A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.
    J Mol Biol, Vol. 331, No. 1. (1 August 2003), pp. 177-189.
    by M Baaden, C Meier, MS Sansom
    posted to channel md membrane ompla simulation by dimka on 2006-02-10 14:08:29 as ** along with 1 person baaden
  • Interaction between K(+) channel gate modifier hanatoxin and lipid bilayer membranes analyzed by molecular dynamics simulation.
    Eur Biophys J, Vol. 35, No. 5. (2 May 2006), pp. 373-381.
    by Manami Nishizawa, Kazuhisa Nishizawa
    posted to structural-modelling simulation md lipid-protein kv by dimka on 2006-02-07 18:23:58 as ***
  • Incorporating the effect of ionic strength in free energy calculations using explicit ions.
    J Comput Chem, Vol. 26, No. 2. (30 January 2005), pp. 115-122.
    by S Donnini, AE Mark, AH Juffer, A Villa
    posted to fep free-energy integration ion ionic-strength md simulation thermodynamics by dimka on 2005-12-14 19:21:16 as **
  • Short-chain phosphatidylinositol conformation and its relevance to phosphatidylinositol-specific phospholipase C
    Biochemistry (John Wiley & Sons), Vol. 36, No. 50. (1997), pp. 15925-15931.
    by C Zhou, V Garigapati, MF Roberts
    posted to simulation resonance phospholipase phosphatidylinositol molecular inhibitor diacylglycerol conformation bonding amp by dimka on 2005-06-06 17:48:08 as **
  • Free energy simulations
    Annals of the New York Academy of Sciences, Vol. 482 (1986), pp. 1-23.
    by M Mezei, DL Beveridge
    posted to method models molecular montecarlo simulation thermodynamics by dimka on 2005-06-06 17:47:58 as **
  • Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
    Biopolymers, Vol. 71, No. 1. (2003), pp. 49-70.
    by I Liepina, C Czaplewski, P Janmey, A Liwo
    posted to pip2 bilayer comparative conformation dimyristoyl gelsolin lipid models molecular pc peptide phosphatidylcholine phosphatidylinositol protein secondary simulation sites structure synthesis by dimka on 2005-06-06 17:47:54 as **
  • Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory
    Journal of Molecular Biology, Vol. 322, No. 4. (2002), pp. 851-869.
    by W Im, B Roux
    posted to diffusion electron models molecular porin simulation structure tertiary by dimka on 2005-06-06 17:47:51 as **
  • Brownian dynamics simulation of protein-protein diffusional encounter
    Methods (San Diego, Calif.), Vol. 14, No. 3. (1998), pp. 329-341.
    by RR Gabdoulline, RC Wade
    posted to bacterial chemical diffusion electrostatics models proteins ribonuclease simulation software by dimka on 2005-06-06 17:47:48 as **
  • Brownian dynamics simulations of interaction between scorpion toxin Lq2 and potassium ion channel
    Biophysical journal, Vol. 80, No. 4. (2001), pp. 1659-1669.
    by M Cui, J Shen, JM Briggs, X Luo, X Tan, H Jiang, K Chen, R Ji
    posted to bonding channel conformation databases electrostatics factual homology hydrogen ligand models molecular potassium protein scorpion secondary sequence simulation sites spectroscopy structure venom by dimka on 2005-06-06 17:47:42 as **
  • A new method for predicting binding affinity in computer-aided drug design
    Protein engineering, Vol. 7, No. 3. (1994), pp. 385-391.
    by J Aqvist, C Medina, JE Samuelsson
    posted to amp antagonist aspartic binding drug-design inhibitor molecular protein simulation sites structure thermodynamics by dimka on 2005-06-06 17:47:30 as **
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