arnaucordomi's library 43 articles Export

	The MARTINI Coarse-Grained Force Field: Extension to Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 5. (1 May 2008), pp. 819-834. by Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, Siewert-Jan Marrink posted to coarsegrain by arnaucordomi on 2009-11-06 10:10:50 as along with 13 people and 3 groups dimka oteri sunrise flbarroso A_Coletta_Thesis krapnik Marine middledomain sobolevnrm Ema aqeel DanielParton softsimu Structural Biology Group TorVergata Molecular dynamics in MSU baker-group
	Conformational complexity of G-protein-coupled receptors [My Copy] Trends in Pharmacological Sciences In Special Issue on Allosterism and Collateral Efficacy, Vol. 28, No. 8. (August 2007), pp. 397-406. by Brian K. Kobilka, Xavier Deupi posted to dimelys by arnaucordomi on 2009-10-01 10:08:59 as along with 3 people guhjy superpyrin psique
	Comparison of multiple Amber force fields and development of improved protein backbone parameters. [My Copy] Proteins, Vol. 65, No. 3. (15 November 2006), pp. 712-725. by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling posted to ffields by arnaucordomi on 2009-09-28 16:20:26 as along with 10 people Vadikus bmduggan baaden lna allmensch choonpeng kazemi barry GermanErlenkamp RamuAnandakrishnan
	Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations [My Copy] The Journal of Chemical Physics, Vol. 127, No. 21. (2007), 214108. by Thomas Steinbrecher, David L. Mobley, David A. Case posted to free-energies by arnaucordomi on 2009-09-15 08:17:03 as along with 2 people and 1 group sobolevnrm dmobley baker-group
	Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems [My Copy] Journal of Computational Chemistry, Vol. 20, No. 8. (5 May 1999), pp. 786-798. by K. Anton Feenstra, Berk Hess, Herman J. C. Berendsen posted to methods md by arnaucordomi on 2009-09-07 08:16:09 as along with 1 person feenstra
	Calculation of the free energy of solvation for neutral analogs of amino acid side chains [My Copy] Journal of Computational Chemistry, Vol. 23, No. 5. (2002), pp. 548-553. by Alessandra Villa, Alan E. Mark posted to methods ffields by arnaucordomi on 2009-09-02 10:48:43 as along with 1 person ashaytan
	Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories [My Copy] Journal of Computational Chemistry, Vol. 29, No. 11. (August 2008), pp. 1740-1752. by Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo posted to methods md by arnaucordomi on 2009-08-27 08:48:57 as along with 2 people and 1 group bmduggan sobolevnrm baker-group
	Isothermal-isobaric molecular dynamics using stochastic velocity rescaling. [My Copy] The Journal of chemical physics, Vol. 130, No. 7. (21 February 2009) by Giovanni Bussi, Tatyana Zykova-Timan, Michele Parrinello posted to methods md by arnaucordomi on 2009-08-26 13:59:48 as
	Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins [My Copy] Journal of Physics: Condensed Matter, Vol. 18, No. 28. (2006), pp. S1221-S1234. by Peter D. Tieleman, Justin L. Maccallum, Walter L. Ash, Christian Kandt, Zhitao Xu, Luca Monticelli posted to membrane-proteins md ffields by arnaucordomi on 2009-08-25 05:38:39 as along with 2 people sunnytov loison
	Setting up and running molecular dynamics simulations of membrane proteins. [My Copy] Methods (San Diego, Calif.), Vol. 41, No. 4. (April 2007), pp. 475-488. by Christian Kandt, Walter L. Ash, D. Peter Tieleman posted to methods md by arnaucordomi on 2009-08-25 05:37:20 as along with 3 people and 2 groups choonpeng xdeupi sobolevnrm LabCompMed baker-group
	Thermodynamics of flip-flop and desorption for a systematic series of phosphatidylcholine lipids [My Copy] Soft Matter (2009) by Nicolas Sapay, Drew W. F. Bennett, Peter D. Tieleman posted to membranes md ffields by arnaucordomi on 2009-08-19 10:26:01 as along with 1 person and 1 group sobolevnrm baker-group
	Effects of alkali cations and halide anions on the DOPC lipid membrane. [My Copy] The journal of physical chemistry. A, Vol. 113, No. 26. (2 July 2009), pp. 7235-7243. by Robert Vácha, Shirley W. Siu, Michal Petrov, et al.Rainer A. Böckmann, Justyna Barucha-Kraszewska, Piotr Jurkiewicz, Martin Hof, Max L. Berkowitz, Pavel Jungwirth posted to membranes md ions ffields by arnaucordomi on 2009-08-18 16:22:37 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension [My Copy] Biophysical Journal, Vol. 92, No. 12. (15 June 2007), pp. 4157-4167. by J. Sonne, M. Jensen, F. Hansen, L. Hemmingsen, G. Peters posted to membranes md ffields by arnaucordomi on 2009-08-13 11:34:11 as along with 1 person dimka
	United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 7. (14 July 2009), pp. 1803-1813. by Jakob P. Ulmschneider, Martin B. Ulmschneider posted to membranes md ffields by arnaucordomi on 2009-08-13 11:26:03 as along with 1 person sobolevnrm
	Amyloid Aggregation on Lipid Bilayers and Its Impact on Membrane Permeability [My Copy] Journal of Molecular Biology, Vol. 387, No. 2. (27 March 2009), pp. 407-415. by Ran Friedman, Riccardo Pellarin, Amedeo Caflisch posted to membranes md by arnaucordomi on 2009-08-13 11:23:00 as along with 1 person paulschlesinger
	The role of fatty acid unsaturation in minimizing biophysical changes on the structure and local effects of bilayer membranes. [My Copy] Biochimica et biophysica acta, Vol. 1788, No. 7. (14 July 2009), pp. 1508-1516. by Sukit Leekumjorn, Hyun Ju J. Cho, Yifei Wu, Neil T. Wright, Amadeu K. Sum, Christina Chan posted to membranes md by arnaucordomi on 2009-08-13 09:43:49 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Canonical sampling through velocity rescaling. [My Copy] The Journal of chemical physics, Vol. 126, No. 1. (7 January 2007), 014101. by Giovanni Bussi, Davide Donadio, Michele Parrinello posted to methods md by arnaucordomi on 2009-08-13 09:43:10 as along with 4 people and 1 group janneb daevans OndrejMarsalek michaelbussmann Soft Matter
	Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 35. (1 September 2006), pp. 17616-17626. by Berk Hess, Nico F. A. van der Vegt posted to ffields md by arnaucordomi on 2009-08-03 14:11:05 as along with 6 people and 1 group softsimu krapnik flbarroso Diego_Prada Marine ashaytan Molecular dynamics in MSU
	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 membranes md ffields by arnaucordomi on 2009-07-31 09:18:54 as along with 3 people and 1 group dimka Marine middledomain Molecular dynamics in MSU
	Structural rearrangements of rhodopsin subunits in a dimer complex: a molecular dynamics simulation study. [My Copy] Journal of biomolecular structure & dynamics, Vol. 27, No. 2. (October 2009), pp. 127-147. by Arnau Cordomí, Juan J. Perez posted to gpcrs md myown oligomers by arnaucordomi on 2009-07-15 09:17:34 as
	New vistas in GPCR 3D structure prediction [My Copy] Journal of Molecular Modeling by Anwar Rayan posted to gpcrs modelling structure by arnaucordomi on 2009-07-08 14:30:01 as along with 1 person xdeupi
	Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Arnau Cordomí, Olle Edholm, Juan J. Perez posted to myown by arnaucordomi on 2009-07-07 07:56:44 as
	Long-chain formoterol analogues: an investigation into the effect of increasing amino-substituent chain length on the beta2-adrenoceptor activity. [My Copy] Bioorganic & medicinal chemistry letters, Vol. 14, No. 18. (20 September 2004), pp. 4705-4710. by V. Alikhani, D. Beer, D. Bentley, et al.I. Bruce, B. M. Cuenoud, R. A. Fairhurst, P. Gedeck, S. Haberthuer, C. Hayden, D. Janus, L. Jordan, C. Lewis, K. Smithies, E. Wissler posted to no-tag by arnaucordomi on 2009-07-01 12:01:42 as
	Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors. [My Copy] Biochemistry (20 April 2009) by Stefano Vanni, Marilisa Neri, Ivano Tavernelli, Ursula Rothlisberger posted to b2ar gpcrs md by arnaucordomi on 2009-07-01 11:11:53 as along with 3 people and 1 group jmccammon agrossfield xdeupi McCammon
	Structure-based discovery of β2-adrenergic receptor ligands [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6843-6848. by Peter Kolb, Daniel M. Rosenbaum, John J. Irwin, Juan J. Fung, Brian K. Kobilka, Brian K. Shoichet posted to b2ar gpcrs ligand-binding by arnaucordomi on 2009-06-30 15:31:40 as along with 2 people npt11tpn reyez
	Acyl chain conformations in phospholipid bilayers: a comparative study of docosahexaenoic acid and saturated fatty acids. [My Copy] Chemistry and physics of lipids, Vol. 153, No. 1. (May 2008), pp. 76-80. by S. E. Feller posted to md membranes by arnaucordomi on 2009-06-30 14:06:20 as along with 1 person and 1 group sobolevnrm baker-group
	The effect of cholesterol on short- and long-chain monounsaturated lipid bilayers as determined by molecular dynamics simulations and X-ray scattering. [My Copy] Biophysical journal, Vol. 95, No. 6. (15 September 2008), pp. 2792-2805. by N. Kucerka, J. D. Perlmutter, J. Pan, S. Tristram-Nagle, J. Katsaras, J. N. Sachs posted to cholesterol membranes by arnaucordomi on 2009-06-30 14:05:14 as along with 1 person paulschlesinger
	Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 31. (1 August 2006), pp. 15045-15048. by Qiang Shi, Sergei Izvekov, Gregory A. Voth posted to cg md by arnaucordomi on 2009-06-30 14:04:14 as along with 3 people flbarroso dimka RamuAnandakrishnan
	On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. [My Copy] Physical chemistry chemical physics : PCCP, Vol. 11, No. 12. (28 March 2009), pp. 1934-1941. by M. Winger, D. Trzesniak, R. Baron, W. F. van Gunsteren posted to cg md by arnaucordomi on 2009-06-30 14:02:57 as along with 4 people and 1 group patvarilly sobolevnrm mbeeby flbarroso baker-group
	The difference between the CB(1) and CB(2) cannabinoid receptors at position 5.46 is crucial for the selectivity of WIN55212-2 for CB(2). [My Copy] Molecular pharmacology, Vol. 56, No. 4. (October 1999), pp. 834-840. by Z. H. Song, C. A. Slowey, D. P. Hurst, P. H. Reggio posted to cb1 gpcrs ligand-binding mutants by arnaucordomi on 2009-06-30 10:48:50 as
	A critical role for a tyrosine residue in the cannabinoid receptors for ligand recognition. [My Copy] Biochemical pharmacology, Vol. 63, No. 12. (15 June 2002), pp. 2121-2136. by S. D. McAllister, Q. Tao, J. Barnett-Norris, et al.K. Buehner, D. P. Hurst, F. Guarnieri, P. H. Reggio, K. W. Nowell Harmon, G. A. Cabral, M. E. Abood posted to cb1 gpcrs ligand-binding mutants by arnaucordomi on 2009-06-30 10:48:11 as
	An aromatic microdomain at the cannabinoid CB(1) receptor constitutes an agonist/inverse agonist binding region. [My Copy] Journal of medicinal chemistry, Vol. 46, No. 24. (20 November 2003), pp. 5139-5152. by S. D. McAllister, G. Rizvi, S. Anavi-Goffer, et al.D. P. Hurst, J. Barnett-Norris, D. L. Lynch, P. H. Reggio, M. E. Abood posted to cb1 gpcrs ligand-binding mutants by arnaucordomi on 2009-06-30 10:47:09 as
	Conformational toggle switches implicated in basal constitutive and agonist-induced activated states of 5-hydroxytryptamine-4 receptors. [My Copy] Molecular pharmacology, Vol. 75, No. 4. (April 2009), pp. 982-990. by L. P. Pellissier, J. Sallander, M. Campillo, et al.F. Gaven, E. Queffeulou, M. Pillot, A. Dumuis, S. Claeysen, J. Bockaert, L. Pardo posted to activation gpcrs toggle-switch by arnaucordomi on 2009-06-29 10:25:43 as along with 1 person xdeupi
	G-protein-coupled receptor structures were not built in a day [My Copy] Protein Science, Vol. 18, No. 7. (20 May 2009), pp. 1335-1342. by Tracy M. Blois, James U. Bowie posted to gpcrs review structure by arnaucordomi on 2009-06-29 10:14:30 as along with 2 people and 1 group lees xdeupi Orengo Group Journal Picks
	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 myown by arnaucordomi on 2009-06-29 10:04:31 as along with 4 people and 1 group robertvacha sobolevnrm softsimu dimka baker-group
	Molecular dynamics simulations of rhodopsin point mutants at the cytoplasmic side of helices 3 and 6. [My Copy] Journal of biomolecular structure & dynamics, Vol. 25, No. 6. (June 2008), pp. 573-587. by A. Cordomí, E. Ramon, P. Garriga, J. J. Perez posted to myown by arnaucordomi on 2009-06-29 09:31:48 as
	Structural characterization of a zinc high-affinity binding site in rhodopsin. [My Copy] Photochemistry and photobiology, Vol. 85, No. 2. (r 2009), pp. 479-484. by D. Toledo, A. Cordomí, M. G. Proietti, et al.M. Benfatto, L. J. del Valle, J. J. Pérez, P. Garriga, F. Sepulcre posted to myown by arnaucordomi on 2009-06-29 09:31:16 as
	Molecular Dynamics Simulations of Rhodopsin in Different One-Component Lipid Bilayers. [My Copy] J Phys Chem B (27 May 2007) by Arnau Cordomí, Juan J. Perez posted to myown by arnaucordomi on 2007-06-07 10:43:52 as along with 1 person softsimu
	Critical role of electrostatic interactions of amino acids at the cytoplasmic region of helices 3 and 6 in rhodopsin conformational properties and activation. [My Copy] J Biol Chem (23 February 2007) by Eva Ramon, Arnau Cordomi, Laia Bosch, et al.Evgeni Yu Y. Zernii, Ivan I I. Senin, Joan Manyosa, Pavel P P. Philippov, Juan J J. Perez, Pere Garriga posted to myown by arnaucordomi on 2007-03-12 08:02:38 as along with 1 person patricia
	X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane. [My Copy] Proteins (31 January 2007) by Francesc Sepulcre, Arnau Cordomí, M Grazia G. Proietti, et al.Juan J J. Perez, Joaquin García, Enric Querol, Esteve Padrós posted to myown by arnaucordomi on 2007-02-20 09:47:32 as
	Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. [My Copy] J Comput Chem (31 January 2007) by Arnau Cordomí, Olle Edholm, Juan J J. Perez posted to myown by arnaucordomi on 2007-02-20 09:46:51 as along with 2 people and 1 group patricia xdeupi LabCompMed
	Study of the conformational profile of the norbornane analogues of phenylalanine. [My Copy] J Pept Sci, Vol. 8, No. 6. (June 2002), pp. 253-266. by A. Cordomí, J. Gomez-Catalan, A. I. Jimenez, C. Cativiela, J. J. Perez posted to myown by arnaucordomi on 2006-11-08 13:01:45 as
	A methyl group at C7 of 11-cis-retinal allows chromophore formation but affects rhodopsin activation. [My Copy] Vision Res (5 October 2006) by Laia Bosch, Arnau Cordomí, Marta Domínguez, et al.Darwin Toledo, Margarita Morillo, Juan J J. Pérez, Rosana Alvarez, Angel R R. de Lera, Pere Garriga posted to myown by arnaucordomi on 2006-11-08 13:00:10 as along with 1 person and 1 group xdeupi LabCompMed

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