Tag molecular-dynamics [at least 200 articles] Export

Recent papers classified by the tag molecular-dynamics.

	Molecular-dynamics investigation of solid--liquid coexistence [My Copy] The Journal of Chemical Physics, Vol. 68, No. 8. (1978), pp. 3401-3404. by Y. Hiwatari, E. Stoll, T. Schneider posted to phase-coexistence molecular-dynamics 1978 by hendysh on 2009-12-05 00:20:44 as
	Molecular modeling of interfaces between cellulose crystals and surrounding molecules: Effects of caprolactone surface grafting [My Copy] European Polymer Journal, Vol. 44, No. 11. (November 2008), pp. 3662-3669. by M. Bergenstrahle, K. Mazeau, L. Berglund posted to surface-tension new molecular-dynamics by dcheong on 2009-11-19 09:23:23 as
	Solid-liquid interface free energy through metadynamics simulations [My Copy] (13 Nov 2009) by Stefano Angioletti-Uberti, Michele Ceriotti, Mike W. Finnis, Peter D. Lee posted to solid-liquid molecular-dynamics free_energy by danilov on 2009-11-16 09:50:46 as
	Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. [My Copy] Journal of molecular graphics, Vol. 12, No. 2. (June 1994), pp. 84-89. by J. Schlitter, M. Engels, P. Krüger posted to targeted molecular-dynamics by bmduggan on 2009-11-07 03:54:58 as
	Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 μs [My Copy] Journal of the American Chemical Society, Vol. 124, No. 44. (1 November 2002), pp. 12952-12953. by Linlin Qiu, Suzette A. Pabit, Adrian E. Roitberg, Stephen J. Hagen posted to trp-cage molecular-dynamics molecular model folding dynamics by zfekete on 2009-11-03 10:06:53 as
	All-Atom Structure Prediction and Folding Simulations of a Stable Protein [My Copy] Journal of the American Chemical Society, Vol. 124, No. 38. (1 September 2002), pp. 11258-11259. by Carlos Simmerling, Bentley Strockbine, Adrian E. Roitberg posted to molecular-dynamics molecular modeling folding dynamics by zfekete on 2009-11-03 10:02:48 as
	Simulating Temperature Jumps for Protein Folding [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 5. (1 February 2008), pp. 1525-1532. by Seonah Kim, Adrian E. Roitberg posted to protein molecular-dynamics molecular modeling folding by zfekete on 2009-11-03 10:00:45 as along with 1 person allmensch
	Computational design of affinity and specificity at protein–protein interfaces [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 4. (29 August 2009), pp. 458-463. by John Karanicolas, Brian Kuhlman posted to rosetta review molecular-dynamics interactions design by bmduggan on 2009-10-28 15:28:08 as along with 4 people sobolevnrm VGreiff higueruelo barry
	Identifying a causal link between structure and dynamics in supercooled water [My Copy] EPL (Europhysics Letters), Vol. 88, No. 1. (2009), 16003. by D. C. Malaspina, J. A. Rodriguez Fris, G. A. Appignanesi, F. Sciortino posted to supercooled structure simulation molecular-dynamics glass by yse on 2009-10-26 20:30:00 as
	Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy [My Copy] Journal of the American Chemical Society, Vol. 129, No. 15. (1 April 2007), pp. 4724-4730. by Phineus R. L. Markwick, Guillaume Bouvignies, Martin Blackledge posted to relaxation rdc molecular-dynamics by rph on 2009-10-26 17:30:55 as along with 2 people bmduggan RamuAnandakrishnan
	Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 4. (29 January 2009), pp. 1162-1172. by Govardhan Reddy, John E. Straub, D. Thirumalai posted to salt-bridge molecular-dynamics alzheimer abeta by zfekete on 2009-10-19 08:10:56 as along with 1 person carlosjavierna
	Structural insights into RNA processing by the human RISC-loading complex [My Copy] Nature Structural & Molecular Biology, Vol. 16, No. 11. (11 October 2009), pp. 1148-1153. by Hong-Wei Wang, Cameron Noland, Bunpote Siridechadilok, et al.David W. Taylor, Enbo Ma, Karin Felderer, Jennifer A. Doudna, Eva Nogales posted to risc molecular-dynamics microrna dicer argonaute by heliopais to the group microRNA on 2009-10-14 09:46:47 as along with 1 person valeriehilgers
	Atomistic and mesoscale simulations of free solidification in comparison [My Copy] Modelling and Simulation in Materials Science and Engineering, Vol. 17, No. 5. (2009), 055006. by Ilya Maltsev, Alexandr Mirzoev, Denis Danilov, Britta Nestler posted to phase-field molecular-dynamics by danilov on 2009-10-07 09:29:26 as
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to proteins molecular-dynamics modelling by kevinchannon on 2009-10-01 16:14:18 as along with 11 people and 3 groups oteri anuragsethi flbarroso r2s2 iantunbridge ihaque sobolevnrm ruvido massivemayhem barry RamuAnandakrishnan baker-group structural_bioinformatics McCammon
	Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 32. (8 August 2006), pp. 11844-11849. by Kei-ichi Okazaki, Nobuyasu Koga, Shoji Takada, Jose N. Onuchic, Peter G. Wolynes posted to molecular-dynamics by bmduggan on 2009-09-23 21:22:27 as along with 3 people and 1 group allmensch choonpeng joseph_x_zhou protein_Dyn
	Onset of patterns in an oscillated granular layer: Continuum and molecular dynamics simulations [My Copy] Physical Review E, Vol. 71, No. 2. (Feb 2005), 021301. by J. Bougie, J. Kreft, J. B. Swift, Harry L. Swinney posted to swift-hohenberg molecular-dynamics granular_media by danilov on 2009-09-21 08:38:00 as
	Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5-ns Molecular Dynamics Simulation [My Copy] Journal of the American Chemical Society, Vol. 124, No. 21. (1 May 2002), pp. 6153-6161. by Kaihsu Tai, Tongye Shen, Richard H. Henchman, Yves Bourne, Pascale Marchot, J. Andrew McCammon posted to molecular-dynamics allostery by bmduggan on 2009-09-15 20:59:29 as along with 1 person ffranca
	Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 961-975. by Scott A. Showalter, Rafael Bruschweiler posted to relaxation nmr molecular-dynamics ff99sb by bmduggan on 2009-09-10 02:12:22 as along with 3 people allmensch pablocarb loison
	Massively parallel computation of absolute binding free energy with well-equilibrated states [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 2. (2009), 021914. by Hideaki Fujitani, Yoshiaki Tanida, Azuma Matsuura posted to new molecular-dynamics free-energy binding by dcheong on 2009-09-09 02:26:45 as
	Bornyl (3,4,5-trihydroxy)-cinnamate--an optimized human neutrophil elastase inhibitor designed by free energy calculations. [My Copy] Bioorganic & medicinal chemistry, Vol. 16, No. 5. (1 March 2008), pp. 2385-2390. by Thomas Steinbrecher, Andrea Hrenn, Korinna L. Dormann, Irmgard Merfort, Andreas Labahn posted to thermodynamic-integration molecular-dynamics interactions docking by bmduggan on 2009-09-08 20:24:03 as along with 1 person dmobley
	A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase. [My Copy] Journal of medicinal chemistry, Vol. 49, No. 6. (23 March 2006), pp. 1837-1844. by Thomas Steinbrecher, David A. Case, Andreas Labahn posted to thermodynamic-integration molecular-dynamics mmpbsa docking by bmduggan on 2009-09-08 20:23:12 as along with 1 person bilab
	Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 4. (1 June 2007), pp. 1096-1112. by Nilesh K. Banavali, Benoît Roux posted to targeted sampling molecular-dynamics interactions allostery by bmduggan on 2009-09-04 15:33:12 as along with 3 people allmensch choonpeng ruvido
	Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. [My Copy] Journal of the American Chemical Society, Vol. 127, No. 40. (12 October 2005), pp. 13778-13779. by Donald Hamelberg, J. Andrew Mccammon posted to molecular-dynamics accelerated by bmduggan on 2009-09-03 20:26:29 as along with 1 person pgasper
	Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study [My Copy] The Journal of Chemical Physics, Vol. 127, No. 17. (2007), 175105. by César Augusto, Donald Hamelberg, J. Andrew Mccammon posted to sampling molecular-dynamics accelerated by bmduggan on 2009-09-03 20:06:57 as along with 1 person and 1 group sobolevnrm baker-group
	Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 10. (10 March 2009), pp. 3776-3781. by Sichun Yang, Nilesh K. Banavali, Benoît Roux posted to sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 19:55:16 as along with 7 people and 2 groups anuragsethi Diego_Prada allmensch guhjy sobolevnrm barry jmccammon baker-group McCammon
	Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. [My Copy] Protein Science, Vol. 7, No. 3. (March 1998), pp. 649-666. by L. S. Caves, J. D. Evanseck, M. Karplus posted to sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 19:43:33 as along with 4 people sunnytov lillekatt allmensch toerst
	Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations [My Copy] Journal of Molecular Biology, Vol. 388, No. 3. (08 May 2009), pp. 644-658. by Anthony Ivetac, J. Andrew Mccammon posted to sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 19:36:44 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	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 sampling molecular-dynamics convergence by bmduggan on 2009-09-03 19:15:38 as along with 11 people and 1 group xdeupi agrossfield allmensch r2s2 apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties. [My Copy] Proteins, Vol. 60, No. 3. (15 August 2005), pp. 464-484. by Xianfeng Li, Sergio A. Hassan, Ernest L. Mehler posted to sampling molecular-dynamics convergence by bmduggan on 2009-09-03 17:16:33 as along with 3 people jjurban flbarroso baaden
	Assessing equilibration and convergence in biomolecular simulations. [My Copy] Proteins, Vol. 48, No. 3. (15 August 2002), pp. 487-496. by Lorna J. Smith, Xavier Daura, Wilfred F. van Gunsteren posted to sampling multicopy molecular-dynamics convergence by bmduggan on 2009-09-03 17:13:38 as along with 3 people and 2 groups sobolevnrm oteri mleis baker-group Structural Biology Group TorVergata
	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 sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 17:11:44 as along with 2 people and 1 group arnaucordomi sobolevnrm baker-group
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted to structure-prediction rosetta molecular-dynamics by bmduggan on 2009-09-02 19:58:03 as along with 16 people and 2 groups newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway ardalby baker-group OPIG
	Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (12 August 2008), pp. 11182-11187. by Kei-ichi Okazaki, Shoji Takada posted to molecular-dynamics allostery by bmduggan on 2009-09-01 20:52:53 as along with 8 people and 2 groups oteri xdeupi okapi aqeel raik ruvido barry zwang structural_bioinformatics McCammon
	Conformational transition pathway in the allosteric process of calcium-induced recoverin: Molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 30, No. 7. (2009), pp. 1135-1145. by Ji-Lai Li, Cai-Yun Geng, Yuxiang Bu, Xu-Ri Huang, Chia-Chung Sun posted to molecular-dynamics allostery by bmduggan on 2009-09-01 20:40:43 as
	On the influence of the initial liquid configuration on the structure of a glass obtained using ab-initio molecular dynamics simulations [My Copy] Journal of Non-Crystalline Solids, Vol. 355, No. 37-42. (01 October 2009), pp. 1807-1810. by Sébastien Le Roux, Philippe Jund posted to structure simulation molecular-dynamics liquid glasses glass ab-initio by yse on 2009-09-01 18:31:14 as
	Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems [My Copy] The Journal of Chemical Physics, Vol. 98, No. 12. (1993), pp. 10089-10092. by Tom Darden, Darrin York, Lee Pedersen posted to molecular-dynamics by bmduggan on 2009-08-31 21:51:02 as along with 13 people anallam sunnytov rpetrenko r2s2 robertvacha A_Coletta_Thesis mleis and_ped10 allmensch easybakemuffin RamuAnandakrishnan tji ashaytan
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to tip3p molecular-dynamics by bmduggan on 2009-08-31 21:24:57 as along with 17 people and 1 group jmparks fralium kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
	Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew [My Copy] The Journal of Chemical Physics, Vol. 120, No. 20. (2004), pp. 9665-9678. by Hans W. Horn, William C. Swope, Jed W. Pitera, et al.Jeffry D. Madura, Thomas J. Dick, Greg L. Hura, Teresa H. Gordon posted to tip4p molecular-dynamics by bmduggan on 2009-08-31 17:23:42 as along with 3 people and 1 group Lombardo_7 whitead softsimu Jiang Research Group
	Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1113-1130. by Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Kim A. Sharp posted to molecular-dynamics ion dna by ras on 2009-08-21 15:12:11 as along with 5 people and 1 group Elena_Zubova sobolevnrm RamuAnandakrishnan onufriev dimka baker-group
	Structure and Dynamics of Surfactant and Hydrocarbon Aggregates on Graphite: A Molecular Dynamics Simulation Study [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 10. (1 March 2008), pp. 2915-2921. by Maria Sammalkorpi, Athanassios Z. Panagiotopoulos, Mikko Haataja posted to surfactants new molecular-dynamics by dcheong on 2009-08-20 10:29:51 as
	A molecular dynamics study of siloxane diffusion in a polyester–melamine solution [My Copy] Polymer, Vol. 48, No. 7. (23 March 2007), pp. 2179-2185. by David J. Henry, Evan Evans, Irene Yarovsky posted to new molecular-dynamics diffusion by dcheong on 2009-08-20 10:27:18 as
	The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrin [My Copy] Protein Science, Vol. 9999, No. 9999. (2009), NA. by Yuanli Song, Nina H. Pipalia, -M posted to leu leucine molecular-dynamics phe phenylalanine by carlosjavierna on 2009-08-05 06:44:18 as
	The shoving model for the glass-former LiCl·6H2O: A molecular dynamics simulation study [My Copy] Journal of Non-Crystalline Solids, Vol. 355, No. 31-33. (01 September 2009), pp. 1659-1662. by Mauro C. C. Ribeiro posted to decoupling glass glasses licl molecular-dynamics by yse on 2009-08-04 19:46:28 as
	Molecular simulations of protein dynamics: new windows on mechanisms in biology. [My Copy] EMBO reports, Vol. 9, No. 2. (February 2008), pp. 144-150. by G. G. Dodson, D. P. Lane, C. S. Verma posted to review molecular-dynamics by bmduggan on 2009-07-28 19:08:33 as
	Protein Side-Chain Dynamics and Residual Conformational Entropy [My Copy] Journal of the American Chemical Society, Vol. 131, No. 2. (21 January 2009), pp. 615-622. by Nikola Trbovic, Jae-Hyun Cho, Robert Abel, Richard A. Friesner, Mark Rance, Arthur G. Palmer posted to molecular-dynamics nmr by bmduggan on 2009-07-27 15:26:07 as along with 2 people and 3 groups barry sobolevnrm structural_bioinformatics McCammon baker-group
	Evaluating Rotational Diffusion from Protein MD Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 19. (1 May 2008), pp. 6013-6024. by Vance Wong, David A. Case posted to tip4p molecular-dynamics by bmduggan on 2009-07-27 15:20:19 as along with 1 person pavanghatty
	Impact of Cl- and Na+ ions on simulated structure and dynamics of βARK1 PH domain [My Copy] Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 206-217. by Stefania Pfeiffer, David Fushman, David Cowburn posted to molecular-dynamics by bmduggan on 2009-07-21 20:54:00 as
	Simulated and NMR-Derived Backbone Dynamics of a Protein with Significant Flexibility: A Comparison of Spectral Densities for the βARK1 PH Domain [My Copy] Journal of the American Chemical Society, Vol. 123, No. 13. (1 April 2001), pp. 3021-3036. by Stefania Pfeiffer, David Fushman, David Cowburn posted to molecular-dynamics nmr relaxation by bmduggan on 2009-07-21 20:52:42 as
	Equivalence of transport coefficients in bath-induced and dynamical scenarios [My Copy] EPL (Europhysics Letters), Vol. 87, No. 1. (2009), 10002. by R. Steinigeweg, M. Ogiewa, J. Gemmer posted to dynmaics granular molecular-dynamics by yse on 2009-07-17 19:08:25 as
	Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8800-8812. by Pavel I. Zhuravlev, Christopher K. Materese, Garegin A. Papoian posted to featured-article molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-13 06:13:40 as along with 1 person and 1 group jmccammon McCammon

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simulation	65
molecular-dynamics-simulations	43
dynamics	23
theory	17
md	12
monte-carlo	12
interactions	11
modeling	10
molecular-modeling	10
pads	10
sampling	10
algorithms	9
nmr	9
spatial-simulation	9
free-energy	8
rheology	8
folding	7
reptation	7
diffusion	6
dna	6
force-field	6
glass	6
glasses	6
molecular	6
physics	6
relaxation	6
review	6
structure	6
biophysics	5
computation	5
docking	5
electrostatics	5
mmpbsa	5
multicopy	5
myoglobin	5
pman	5
systems-biology	5
allostery	4
constant-ph	4
essential-dynamics	4
gromacs	4
hyperdynamics	4
multi-scale	4
new	4
replica-exchange	4
soft_potential	4
tprop	4
accelerated	3
bilayers	3
convergence	3
factorx	3
g0-me	3
ihpc	3
isomerization	3
liquid	3
liquid-crystal	3
model	3
nanotubes	3
protein	3
roux	3
sliplink	3
water	3
ala	2
amber	2
amino-acids	2
argonaute	2
artifacts	2
carbon-nanotubes	2
cellulosome	2
coarse-grain	2
cohesin	2
decoupling	2
espresso	2
evaporation	2
featured-article	2
force-fields	2
gay-berne	2
go-models	2
granular	2
hiv-protease	2
lennard-jones	2
leu	2
micelles	2
microrna	2
multipole	2
nematic	2
particle-mesh-ewald	2
polarizability	2
polycarbonate	2
rosetta	2
roux-benoit	2
salt-bridge	2
simulated-annealing	2
simulations	2
surface-tension	2
targeted	2
thermodynamic-integration	2
tip4p	2
tissuefactor	2
trp-cage	2

Tag molecular-dynamics [at least 200 articles] Export

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