Tag md [more than 800 articles] Export

Recent papers classified by the tag md.

	Ion specific correlations in bulk and at biointerfaces [My Copy] J. Phys. Condens. Matter, Vol. 21, No. 42. (2009), 424108. by I. Kalcher, D. Horinek, R. R. Netz, J. Dzubiella posted to md ionpair hofmeister by mikaellund on 2009-11-05 10:39:59 as
	High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000528. by Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, et al.Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji posted to md highthroughput docking bindingaffinities by ibuch on 2009-11-05 09:26:58 as along with 5 people and 1 group klexa skywalkerus02 kentsis reyez barry McCammon
	NMR spectroscopy brings invisible protein states into focus [My Copy] Nature Chemical Biology, Vol. 5, No. 11. (19 October 2009), pp. 808-814. by Andrew J. Baldwin, Lewis E. Kay posted to md folding by flbarroso on 2009-11-04 17:28:19 as along with 1 person paulschlesinger
	Exploring the Free Energy Landscape: From Dynamics to Networks and Back [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000415. by Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique, Fernando Falo posted to md fes by Fernando_FF on 2009-11-03 17:20:26 as along with 6 people sobolevnrm kiekyon phoenixzxl edws zwang Diego_Prada
	Water Structure at Solid Surfaces of Varying Hydrophobicity [My Copy] The Journal of Physical Chemistry C, Vol. 0, No. 0. (0000) by Travis G. Trudeau, Kailash C. Jena, Dennis K. Hore posted to water md by Fernando_FF on 2009-11-03 17:15:41 as along with 1 person qshao
	Cell therapy strategies and improvements for muscular dystrophy [My Copy] Cell Death & Differentiation, Vol. aop, No. current. (30 October 2009) by M. Quattrocelli, M. Cassano, S. Crippa, I. Perini, M. Sampaolesi posted to stem quatt09pdf md managment cell apoptosis by paulschlesinger on 2009-11-01 02:04:18 as
	Investigating interactions between HIV-1 gp41 and inhibitors by molecular dynamics simulation and MM–PBSA/GBSA calculations [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 766, No. 2-3. (15 August 2006), pp. 77-82. by Jian J. Tan, Wei Z. Chen, Cun X. Wang posted to modeling md by mijogiffin on 2009-10-31 15:40:14 as along with 1 person and 1 group sobolevnrm baker-group
	Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. [My Copy] Journal of computer-aided molecular design, Vol. 19, No. 11. (November 2005), pp. 765-770. by Christophe Chipot, Xavier Rozanska, Surjit B. Dixit posted to modeling md by mijogiffin on 2009-10-31 15:38:49 as
	Biomolecular modeling: Goals, problems, perspectives. [My Copy] Angewandte Chemie (International ed. in English), Vol. 45, No. 25. (19 June 2006), pp. 4064-4092. by Wilfred F. van Gunsteren, Dirk Bakowies, Riccardo Baron, et al.Indira Chandrasekhar, Markus Christen, Xavier Daura, Peter Gee, Daan P. Geerke, Alice Glättli, Philippe H. Hünenberger, Mika A. Kastenholz, Chris Oostenbrink, Merijn Schenk, Daniel Trzesniak, Nico F. van der Vegt, Haibo B. Yu posted to modeling md by mijogiffin on 2009-10-31 15:38:20 as along with 2 people patricia LamBras
	Replica-exchange molecular dynamics method for protein folding [My Copy] Chemical Physics Letters, Vol. 314, No. 1-2. (26 November 1999), pp. 141-151. by Y. Sugita posted to replica md exchange by chemrahul82 on 2009-10-29 23:37:54 as along with 8 people and 1 group tovrstra Diego_Prada oteri Sylvain_Prigent andreasauerwein dgront allmensch rulix Structural Biology Group TorVergata
	[capital Psi][CH(CF3)NH]Gly-peptides: synthesis and conformation analysis [My Copy] Org. Biomol. Chem., Vol. 7, No. 11. (2009), pp. 2286-2296. by Marco Molteni, Maria C. Bellucci, Serena Bigotti, Stefania Mazzini, Alessandro Volonterio, Matteo Zanda posted to peptidomimetic md conformation_analysis by jjurban on 2009-10-29 19:32:16 as
	Molecular dynamics simulations of polyamidoamine dendrimers and their complexes with linear poly(ethylene oxide) at different pH conditions: static properties and hydrogen bonding [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 43. (2009), pp. 10017-10028. by I. Tanis, K. Karatasos posted to simulation md dendrimer by qshao on 2009-10-29 17:36:36 as
	All-Atom Molecular Dynamics Study of a Spherical Micelle Composed of N-Acetylated Poly(ethylene glycol)−Poly(γ-benzyl l-glutamate) Block Copolymers: A Potential Carrier of Drug Delivery Systems for Cancer [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Hiroshi Kuramochi, Yoshimichi Andoh, Noriyuki Yoshii, Susumu Okazaki posted to md copolymer assemble by qshao on 2009-10-27 16:48:34 as
	The Key Event in Force-Induced Unfolding of Titins Immunoglobulin Domains [My Copy] Vol. 79, No. 1. (1 July 2000), pp. 51-65. by Hui Lu, Klaus Schulten posted to unfolding titin proteins md by edws on 2009-10-26 07:58:57 as
	Clustering of Glycine Molecules in Aqueous Solution Studied by Molecular Dynamics Simulation [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 24. (1 June 2008), pp. 7280-7288. by Said Hamad, Colan E. Hughes, Catlow, Kenneth D. M. Harris posted to zwitterion molecular_dynamics md glyine glycine_dimer glycine by whitead to the group Jiang Research Group on 2009-10-26 06:13:40 as
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted to mmpbsa md by mijogiffin on 2009-10-25 19:56:40 as along with 15 people and 3 groups flbarroso GermanErlenkamp onufriev arlam oteri jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi Chang group Structural Biology Group TorVergata McCammon
	Free energy perturbation and molecular dynamics calculations of copper binding to azurin [My Copy] Journal of Computational Chemistry, Vol. 24, No. 6. (2003), pp. 779-785. by Matteo Pappalardo, Danilo Milardi, Domenico M. Grasso, Carmelo La Rosa posted to md by mijogiffin on 2009-10-25 19:49:27 as
	Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin. [My Copy] Journal of molecular modeling, Vol. 15, No. 8. (August 2009), pp. 959-969. by Saravana Prakash P. Thirumuruganandham, Herbert M. Urbassek posted to membrane_proteins md flexibility energy_landscape dynamics disorder by xdeupi on 2009-10-25 11:22:15 as along with 2 people saravan gcaltabiano
	Correct virial formulation in the isotropic periodic sum method [My Copy] The Journal of Chemical Physics, Vol. 131, No. 16. (2009), 164103. by Iordan H. Hristov, Reginald Paul, Stephen J. Paddison posted to md by RamuAnandakrishnan on 2009-10-24 01:37:53 as
	Effect of Ions on the Hydrophobic Interaction between Two Plates [My Copy] Journal of the American Chemical Society, Vol. 129, No. 15. (1 April 2007), pp. 4678-4686. by Ronen Zangi, Morten Hagen, B. J. Berne posted to md hydrophobic hofmeister by mikaellund on 2009-10-23 23:21:22 as along with 1 person and 1 group samjlord moernerlab
	Molecular dynamics simulation of water confined in a nanopore of amorphous silica [My Copy] Molecular Simulation, Vol. 35, No. 15. (2009), pp. 1215-1223. by Qingyin Zhang, Kwong-Yu Chan, Nicholas Quirke posted to silica_material md amorphous by flbarroso on 2009-10-21 14:41:30 as
	Isotropic periodic sum: A method for the calculation of long-range interactions [My Copy] The Journal of Chemical Physics, Vol. 122, No. 4. (2005), 044107. by Xiongwu Wu, Bernard R. Brooks posted to md electrostatic by mikaellund on 2009-10-21 09:36:42 as
	Isotropic periodic sum of electrostatic interactions for polar systems [My Copy] The Journal of Chemical Physics, Vol. 131, No. 2. (2009), 024107. by Xiongwu Wu, Bernard R. Brooks posted to md electrostatic by mikaellund on 2009-10-21 09:34:42 as along with 2 people agrossfield dlimmer
	Molecular Dynamics on Interface and Nanoscratch Mechanisms of Alkanethiol Self-Assembled Monolayers [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Wen-Yang Chang, Te-Hua Fang, Chun-Nan Fang posted to md friction by qshao on 2009-10-16 18:00:30 as
	Harvesting graphics power for MD simulations [My Copy] Molecular Simulation, Vol. 34, No. 3. (2008), pp. 259-266. by J. A. van Meel, A. Arnold, D. Frenkel, Portegies, R. G. Belleman posted to molecular modeling md dynamics by zfekete on 2009-10-16 15:27:35 as along with 3 people tomhebbron dgront michaelbussmann
	Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 8. (June 2009), pp. 889-899. by Elena Papaleo, Paolo Mereghetti, Piercarlo Fantucci, Rita Grandori, Luca De Gioia posted to pca md analyais by dimka on 2009-10-14 23:51:37 as along with 1 person anuragsethi
	Discovery Through the Computational Microscope [My Copy] Vol. 17, No. 10. (14 October 2009), pp. 1295-1306. by Eric H. Lee, Jen Hsin, Marcos Sotomayor, Gemma Comellas, Klaus Schulten posted to md by agrossfield on 2009-10-13 19:54:19 as along with 1 person anuragsethi
	Thermodynamic Perspective on the Dock−Lock Growth Mechanism of Amyloid Fibrils [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Edward P. O’Brien, Yuko Okamoto, John E. Straub, Bernard R. Brooks, D. Thirumalai posted to urea tmao solvent simulation md implicit fibril explicit amyloid aggregation by samcho on 2009-10-12 15:29:56 as
	Analysis of dissociation process for gas hydrates by molecular dynamics simulation [My Copy] Molecular Simulation (2009) by Yoshio Iwai, Hiroki Nakamura, Yuki Arai, Yusuke Shimoyama posted to md dissociation by flbarroso on 2009-10-09 22:18:27 as
	Long-timescale molecular dynamics simulations of protein structure and function. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (08 April 2009), pp. 120-127. by John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, David E. Shaw posted to review md by xdeupi on 2009-10-08 11:13:56 as along with 11 people and 1 group agrossfield allmensch bmduggan r2s2 apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 12. (24 March 2009), pp. 4689-4694. by Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, David E. Shaw posted to theory structure modeling md flexibility dynamics b2ar activation by xdeupi on 2009-10-08 11:13:04 as along with 2 people dimka agrossfield
	Structural stability of electrosprayed proteins: temperature and hydration effects [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 36. (2009), pp. 8069-8078. by Erik G. Marklund, Daniel S. D. Larsson, David Spoel, Alexandra Patriksson, Carl Caleman posted to protein md hydration electrophoresis by flbarroso on 2009-10-07 17:51:04 as
	Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (3 April 2009), e1000343. by Bosco K. Ho, David A. Agard posted to perturbation_method molecular_dynamics md conformational_changes allostery by skywalkerus02 on 2009-10-07 06:29:23 as along with 5 people and 3 groups dimka operon sobolevnrm barry bourby baker-group structural_bioinformatics McCammon
	Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists. [My Copy] Proteins (12 August 2009) by Brajesh K. Rai, Gregory J. Tawa, Alan H. Katz, Christine Humblet posted to theory modeling md gpcr by xdeupi on 2009-10-06 19:31:07 as
	Exploring Molecular Mechanisms of Ligand Recognition by Opioid Receptors with Metadynamics. [My Copy] Biochemistry (28 September 2009) by Davide Provasi, Andrea Bortolato, Marta Filizola posted to pathways md binding_kinetics binding by xdeupi on 2009-10-06 19:30:24 as
	Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. [My Copy] Proteins, Vol. 76, No. 2. (1 August 2009), pp. 403-417. by George Khelashvili, Alan Grossfield, Scott E. Feller, Michael C. Pitman, Harel Weinstein posted to theory rhodopsin md cholesterol by xdeupi on 2009-10-06 18:06:55 as along with 1 person and 1 group sobolevnrm baker-group
	Simulation of the structure and dynamics of nonhelical RNA motifs [My Copy] Current Opinion in Structural Biology, Vol. 10, No. 3. (01 June 2000), pp. 311-317. by M. Zacharias posted to simulation rna protein md interaction by aditi9783 on 2009-10-05 20:58:28 as
	A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 [My Copy] Journal of Computational Chemistry, Vol. 25, No. 13. (2004), pp. 1656-1676. by Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. Van Gunsteren posted to md forcefield by dsmueller on 2009-10-05 14:25:41 as along with 6 people loison peyamin rodrigofaccioli whitead tji ashaytan
	“Ab initio” liquid water [My Copy] The Journal of Chemical Physics, Vol. 99, No. 11. (1993), pp. 9080-9089. by K. Laasonen, M. Sprik, M. Parrinello, R. Car posted to water md by dsmueller on 2009-10-05 14:14:43 as
	Charge equilibration for molecular dynamics simulations [My Copy] The Journal of Physical Chemistry, Vol. 95, No. 8. (1 April 1991), pp. 3358-3363. by Anthony K. Rappe, William A. Goddard III posted to md by dsmueller on 2009-10-05 14:10:31 as along with 1 person loison
	Coarse Grained Model for Semiquantitative Lipid Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 108, No. 2. (1 January 2004), pp. 750-760. by Siewert J. Marrink, Alex H. de Vries, Alan E. Mark posted to membrane md by dsmueller on 2009-10-05 14:06:44 as along with 5 people and 1 group Elena_Zubova Marine choonpeng softsimu sunnytov Molecular dynamics in MSU
	Mechanical unfolding intermediates in titin modules [My Copy] Nature, Vol. 402, No. 6757. (04 November 1999), pp. 100-103. by Piotr E. Marszalek, Hui Lu, Hongbin Li, et al.Mariano Carrion-Vazquez, Andres F. Oberhauser, Klaus Schulten, Julio M. Fernandez posted to protein md by dsmueller on 2009-10-05 14:02:47 as along with 2 people grahamc choonpeng
	Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient-corrected density functionals [My Copy] The Journal of Chemical Physics, Vol. 105, No. 3. (1996), pp. 1142-1152. by Michiel Sprik, Jürg Hutter, Michele Parrinello posted to water md by dsmueller on 2009-10-05 13:56:38 as
	Torsion angle dynamics for NMR structure calculation with the new program D$_YANA$ [My Copy] Journal of Molecular Biology, Vol. 273, No. 1. (17 October 1997), pp. 283-298. by P. Güntert, C. Mumenthaler, K. Wüthrich posted to nmr md by dsmueller on 2009-10-05 13:29:01 as along with 5 people ras stharward babakap BragilMassoud lna
	All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 18. (1 April 1998), pp. 3586-3616. by A. D. MacKerell, D. Bashford, M. Bellott, et al.R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to md forcefield by dsmueller on 2009-10-05 13:03:05 as along with 12 people jmparks rpetrenko jrperillaj Diego_Prada oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill ssomani
	Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules [My Copy] Physical Review, Vol. 159, No. 1. (5 Jul 1967), pp. 98-103. by Loup Verlet posted to md by dsmueller on 2009-10-04 12:18:45 as along with 6 people georgwachter stephenbond theschwartz and_ped10 OndrejMarsalek maburkitt
	Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Roland Schulz, Benjamin Lindner, Loukas Petridis, Jeremy C. Smith posted to md by RamuAnandakrishnan on 2009-09-30 00:03:39 as along with 1 person r2s2
	Molecular dynamics simulations of AOT reverse micelles' self-assembly [My Copy] Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, Vol. 107, No. 20. (2009), pp. 2169-2180. by Alexander V. Nevidimov, Vladimir F. Razumov posted to micelles md aot by flbarroso on 2009-09-28 20:52:43 as
	Identification of dynamic structural domains in proteins, analysis of local bond flexibility and application for interpretation of NMR experiments [My Copy] Molecular Simulation (2009) by Maria Stepanova posted to protein_g prion_proteins nmr_experiments nmr md flexibility drug-design bioinformatics by flbarroso on 2009-09-26 05:01:07 as
	One-Dimensional Barrier-Preserving Free-Energy Projections of a β-sheet Miniprotein: New Insights into the Folding Process [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 29. (1 July 2008), pp. 8701-8714. by Sergei V. Krivov, Stefanie Muff, Amedeo Caflisch, Martin Karplus posted to profile md landscape folding by ruvido on 2009-09-24 14:26:46 as

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simulation	127
dynamics	76
membrane	69
electrostatics	60
protein	59
folding	49
lipid	46
modeling	44
water	42
coarse-grained	34
implicit_solvent	34
structure	31
binding	29
molecular	29
simulations	29
nmr	28
qmmm	28
rhodopsin	28
urea	26
review	24
kremer	23
amber	22
activation	19
flexibility	19
md_history	19
mscproject	19
methods	18
peptide	18
free_energy	17
grest	17
unfolded_protein	17
docking	16
forcefield	16
gpcr	16
theodorou	16
force-fields	15
fullatom	14
moleculardynamics	14
pca	14
potential	14
theory	14
amyloid	13
swnt	13
force_field	12
free-energy	12
gromacs	12
model	12
molecular-dynamics	12
primitive_path	12
qm	12
bacteriorhodopsin	11
coarse_grain	11
dce	11
polyethylene	11
protein-protein	11
proteins	11
text_book	11
algorithm	10
algorithms	10
channel	10
cytochrome	10
diffusion	10
helix	10
lysozyme	10
molecular-dynamics-simulations	10
transmembrane	10
aggregation	9
atomic_level_stress	9
bilayer	9
continnum	9
entanglement	9
kroger	9
modelling	9
c	8
computation	8
cutoff	8
dppc	8
force	8
gpu	8
hpc	8
kir	8
lipids	8
masters	8
membranes	8
method	8
polarizable	8
prediction	8
protein_dynamics	8
proteinligand	8
rna	8
targeted_md	8
unentangled_polymer	8
ab-initio	7
coarse-grain	7
dmpc	7
dna	7
explicit_solvent	7
hartree-fock	7
polystyrene	7
unfolding	7

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