dimka's simulation [47 articles] Export

Recent papers added to dimka's library classified by the tag simulation. You can also see everyone's simulation.

	Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach. [My Copy] Biophysical journal, Vol. 88, No. 2. (1 February 2005), pp. 805-817. by Ryan W. Benz, Francisco Castro-Román, Douglas J. Tobias, Stephen H. White posted to simulation lipid charmm27 charmm22 bilayer by dimka on 2009-09-16 21:09:13 as along with 2 people nbrayali softsimu
	Molecular Dynamics Simulations of PIP2 and PIP3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Roughness on a Poisson-Boltzmann Description [My Copy] Biophysical Journal, Vol. 97, No. 1. (08 July 2009), pp. 155-163. by Zheng Li, Richard M. Venable, Laura A. Rogers, Diana Murray, Richard W. Pastor posted to bilayer lipid md pip2 pip3 simulation by dimka on 2009-07-08 21:33:21 as
	Perturbations of membrane structure by cholesterol and cholesterol derivatives are determined by sterol orientation. [My Copy] Journal of the American Chemical Society, Vol. 131, No. 13. (8 April 2009), pp. 4854-4865. by Brett N. Olsen, Paul H. Schlesinger, Nathan A. Baker posted to cholesterol lipid md popc simulation by dimka on 2009-06-30 20:49:00 as along with 2 people and 1 group sunnytov sobolevnrm baker-group
	Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 27. (9 July 2009), pp. 9183-9196. by Joseph E. Davis, Sandeep Patel posted to c27r dmpc dppc md simulation by dimka on 2009-06-19 19:28:42 as along with 1 person agrossfield
	Short-Chain Phosphatidylinositol Conformation and Its Relevance to Phosphatidylinositol-Specific Phospholipase C† [My Copy] Biochemistry, Vol. 36, No. 50. (1 December 1997), pp. 15925-15931. by Chun Zhou, Venkata Garigapati, Mary F. Roberts posted to amp bonding dag headgroup inositiol orientation phosphatidylinositol plc simulation by dimka on 2009-04-14 18:36:26 as
	Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 3. (10 March 2009), pp. 615-626. by Andreas Kukol posted to bilayer lipid md order-parameter simulation by dimka on 2009-04-06 22:31:56 as along with 3 people and 1 group arnaucordomi Marine middledomain Molecular dynamics in MSU
	Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble [My Copy] Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1788, No. 3. (1 March 2009), pp. 638-649. by J. Taylor, N. Whiteford, G. Bradley, G. Watson posted to analysis bilayer charmm dppc gromacs pdpc popc simulation by dimka on 2009-03-27 20:33:17 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Effects of fatty acid inclusion in a DMPC bilayer membrane. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 1. (8 January 2009), pp. 92-102. by G. H. Peters, F. Y. Hansen, M. S. Møller, P. Westh posted to bilayer cholesterol dmpc lipid membrane simulation by dimka on 2009-03-11 19:24:40 as
	Chapter 12 Molecular Modeling and Simulation Studies of Ion Channel Structures, Dynamics and Mechanisms [My Copy] In Methods in Nano Cell Biology, Vol. 90 (2008), pp. 233-265. by Kaihsu Tai, Philip Fowler, Younes Mokrab, Phillip Stansfeld, Mark S. Sansom posted to kir review simulation by dimka on 2009-03-09 18:01:24 as
	Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (20 February 2009), e1000289. by Pär Bjelkmar, Perttu S. Niemelä, Ilpo Vattulainen, Erik Lindahl posted to gromacs kv12 popc popg simulation by dimka on 2009-02-24 22:51:28 as along with 2 people Vadikus blasco_morozzo
	Performance of the general amber force field in modeling aqueous POPC membrane bilayers [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058. by Balázs Jójárt, Tamás A. Martinek posted to amber lipid md membrane simulation by dimka on 2008-11-11 21:48:17 as along with 3 people and 1 group xdeupi easybakemuffin viktor21614 LabCompMed
	Hydration forces between phospholipid bilayers [My Copy] Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, Vol. 988, No. 3. (06 December 1989), pp. 351-376. by R. Rand posted to equilibration lipid md membrane review simulation by dimka on 2008-10-29 00:10:07 as along with 2 people scampos softsimu
	Molecular dynamics simulation of hydrated phospholipid bilayers. [My Copy] Indian journal of biochemistry & biophysics, Vol. 33, No. 6. (December 1996), pp. 431-447. by V. Kothekar posted to dmpc lipid md membrane simulation by dimka on 2008-08-20 19:33:30 as
	Cholesterol Packing around Lipids with Saturated and Unsaturated Chains: A Simulation Study [My Copy] Langmuir (3 June 2008) by Sagar A. Pandit, See-Wing Chiu, Eric Jakobsson, Ananth Grama, H. L. Scott posted to cholesterol dopc md simulation by dimka on 2008-08-18 22:53:18 as along with 2 people and 1 group paulschlesinger sobolevnrm baker-group
	Effective Mast Cell Degranulating Peptide Inhibitors of the IgE/FcepsilonRI Receptor Interaction. [My Copy] Chemical biology & drug design (3 July 2008) by Angeliki Buku, Inna Keselman, Dmitry Lupyan, Mihaly Mezei, Joseph A A. Price posted to ige ige-receptor mcd md peptide simulation by dimka on 2008-07-29 21:44:13 as along with 1 person yanz
	Mechanism of Na+/H+ Antiporting [My Copy] Science, Vol. 317, No. 5839. (10 August 2007), pp. 799-803. by Isaiah T. Arkin, Huafeng Xu, Morten O. Jensen, et al.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 desmond md membrane simulation by dimka on 2008-07-08 21:34:50 as along with 6 people and 1 group Diego_Prada allmensch sobolevnrm Jporci MMehrotra LamBras baker-group
	Conformational Changes and Gating at the Selectivity Filter of Potassium Channels [My Copy] J. Am. Chem. Soc. (28 June 2008) by Carmen Domene, Michael L. Klein, Davide Branduardi, Francesco L. Gervasio, Michele Parrinello posted to kirbac lipid md selectivity simulation 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 [My Copy] 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 compare md membrane protein simulation by dimka on 2008-06-25 16:48:52 as
	Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study [My Copy] 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 lipid md nanotube perturbation simulation by dimka on 2008-05-13 21:14:16 as along with 2 people Marine loison
	Focus on Kir6.2: a key component of the ATP-sensitive potassium channel. [My Copy] Journal of molecular and cellular cardiology, Vol. 38, No. 6. (June 2005), pp. 927-936. by S. Haider, J. F. Antcliff, P. Proks, M. S. Sansom, F. M. Ashcroft posted to atp katp kir62 md simulation by dimka on 2008-05-09 21:33:30 as
	Homology Modeling and Molecular Dynamics Simulation Studies of an Inward Rectifier Potassium Channel [My Copy] 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 kcsa kir permeation simulation tertiapin by dimka on 2008-05-09 20:40:16 as
	Effect of Ions on a Dipalmitoyl Phosphatidylcholine Bilayer. A Molecular Dynamics Simulation Study [My Copy] J. Phys. Chem. B (15 January 2008) by A. Cordomi, O. Edholm, J. J. Perez posted to dppc lipid lipid-area simulation by dimka on 2008-05-08 23:58:41 as along with 4 people and 1 group arnaucordomi robertvacha sobolevnrm softsimu baker-group
	Molecular dynamics simulations of potassium channels [My Copy] Central European Journal of Chemistry, Vol. 5, No. 3. (2007), pp. 635-671. by Carmen Domene posted to channels kir md review simulation by dimka on 2008-05-08 23:28:34 as
	Biological Membranes: A Molecular Perspective from Computation and Experiment [My Copy] (30 July 1996) by Kenneth Merz, Benoit Roux posted to lipid membrane simulation by dimka on 2008-05-07 07:29:15 as
	Electrostatic contribution to the surface pressure of charged monolayers containing polyphosphoinositides [My Copy] Biophys. J. (25 April 2008), biophysj.107.126615. by Ilya Levental, Paul A. Janmey, Andrejs Cebers posted to calculation pi pip2 simulation 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 [My Copy] J. Am. Chem. Soc. (23 February 2008) by C. Domene, S. Vemparala, S. Furini, K. Sharp, M. L. 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 [My Copy] Biochemistry, Vol. 43, No. 28. (20 July 2004), pp. 9009-9020. by K. Kaur, L. C. Andrew, D. S. Wishart, J. C. 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 [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15323-15327. by V. V. Volkov, R. Chelli, W. Zhuang, et al.F. Nuti, Y. Takaoka, A. M. 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 [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 3. (16 January 2007), pp. 796-801. by Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, et al.Alberto Pérez, Jordi Camps, Adam Hospital, Josep L. Gelpí, Modesto Orozco posted to benchmark md simulation by dimka on 2007-02-19 23:50:00 as along with 14 people and 1 group Diego_Prada bmduggan lna aqeel aswin rabio grahamc hmk zwang biehl Ema phoenixzxl ras LamBras The BMM Dome
	Ion Conduction through MscS as Determined by Electrophysiology and Simulation. [My Copy] Biophys J, Vol. 92, No. 3. (17 February 2007), pp. 886-902. 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. [My Copy] J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 47. (30 November 2006), pp. 24157-24164. by F. Castro-Roman, R. W. Benz, S. H. White, D. J. Tobias posted to dopc lipid simulation by dimka on 2006-11-28 20:18:25 as along with 1 person nbrayali
	Effect of Cholesterol on the Properties of Phospholipid Membranes. 4. Interatomic Voids. [My Copy] 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 lipid md membrane simulation by dimka on 2006-07-27 21:25:14 as
	Molecular Dynamics study of MscL interactions with a curved lipid bilayer. [My Copy] Biophys J (2 June 2006) by Grischa R R. Meyer, Justin Gullingsrud, Klaus Schulten, Boris Martinac posted to lipid md mechanosensitive membrane mscl simulation by dimka on 2006-06-09 18:38:04 as along with 1 person choonpeng
	Model for the structure of the lipid bilayer. [My Copy] Proc Natl Acad Sci U S A, Vol. 88, No. 3. (1 February 1991), pp. 892-896. by R. W. Pastor, R. M. 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 [My Copy] 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. [My Copy] Protein science : a publication of the Protein Society, 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 along with 8 people and 2 groups tomjad awarlau ana iakes jwm analogAI sebk tjimenez structural_bioinformatics Bioinformatics
	A molecular dynamics study of an archaeal tetraether lipid membrane: comparison with a dipalmitoylphosphatidylcholine lipid bilayer. [My Copy] Lipids, Vol. 40, No. 10. (October 2005), pp. 1023-1030. by J. P. Nicolas posted to dppc membrane simulation by dimka on 2006-03-06 16:16:42 as
	BioShella package of tools for structural biology computations [My Copy] 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. [My Copy] J Mol Biol, Vol. 331, No. 1. (1 August 2003), pp. 177-189. by M. Baaden, C. Meier, M. S. 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. [My Copy] Eur Biophys J, Vol. 35, No. 5. (2 May 2006), pp. 373-381. by Manami Nishizawa, Kazuhisa Nishizawa posted to kv lipid-protein md simulation structural-modelling by dimka on 2006-02-07 18:23:58 as
	Incorporating the effect of ionic strength in free energy calculations using explicit ions. [My Copy] J Comput Chem, Vol. 26, No. 2. (30 January 2005), pp. 115-122. by S. Donnini, A. E. Mark, A. H. 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
	Free energy simulations [My Copy] Annals of the New York Academy of Sciences, Vol. 482 (1986), pp. 1-23. by M. Mezei, D. L. 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 [My Copy] Biopolymers, Vol. 71, No. 1. (2003), pp. 49-70. by I. Liepina, C. Czaplewski, P. Janmey, A. Liwo posted to conformation dimyristoyl gelsolin lipd models molecular pc peptide phosphatidylcholine phosphatidylinositol pi pip2 simulation 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 [My Copy] 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 [My Copy] Methods (San Diego, Calif.), Vol. 14, No. 3. (1998), pp. 329-341. by R. R. Gabdoulline, R. C. 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 [My Copy] Biophysical journal, Vol. 80, No. 4. (2001), pp. 1659-1669. by M. Cui, J. Shen, J. M. Briggs, et al.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 [My Copy] Protein engineering, Vol. 7, No. 3. (1994), pp. 385-391. by J. Aqvist, C. Medina, J. E. 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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md	100
pip2	100
channel	85
structure	84
lipid	81
membrane	72
kir	61
protein	61
mmult-ref	60
gating	47
simulation	47
molecular	44
phosphatidylinositol	38
potassium	38
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review	37
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kir11	12
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triphosphate	11
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free-energy	10
girk	10
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kinetics	10
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chloride	1
circadian	1
circular_variance	1
clasification	1
cloning	1
close	1
coated	1

dimka's simulation [47 articles] Export

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