agrossfield's library 351 articles Export

	A soft-core Gay--Berne model for the simulation of liquid crystals by Hamiltonian replica exchange [My Copy] The Journal of Chemical Physics, Vol. 131, No. 17. (2009), 174107. by Roberto Berardi, Claudio Zannoni, Juho S. Lintuvuori, Mark R. Wilson posted to replica-exchange coarse-grain by agrossfield on 2009-11-06 20:34:51 as
	Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure [My Copy] Vol. 97, No. 9. (4 November 2009), pp. 2541-2549. by Hannes H. Loeffler, Akio Kitao posted to pca by agrossfield on 2009-11-04 02:00:22 as
	Helical Conformation of the SEVI Precursor Peptide PAP248-286, a Dramatic Enhancer of HIV Infectivity, Promotes Lipid Aggregation and Fusion [My Copy] Vol. 97, No. 9. (4 November 2009), pp. 2474-2483. by Jeffrey R. Brender, Kevin Hartman, Lindsey M. Gottler, Marchello E. Cavitt, Daniel W. Youngstrom, Ayyalusamy Ramamoorthy posted to sevi membrane-fusion hiv_virus by agrossfield on 2009-11-04 01:59:54 as
	Structure of Chemokine-Derived Antimicrobial Peptide Interleukin-8α and Interaction with Detergent Micelles and Oriented Lipid Bilayers [My Copy] Biochemistry, Vol. 48, No. 44. (10 November 2009), pp. 10509-10521. by Sarah Bourbigot, Liam Fardy, Alan J. Waring, Michael R. Yeaman, Valerie Booth posted to antimicrobial-peptide by agrossfield on 2009-11-03 19:12:09 as
	Spatial updating in the great grand canonical ensemble [My Copy] The Journal of Chemical Physics, Vol. 131, No. 16. (2009), 161106. by G. Orkoulas, Daniel P. Noon posted to grand_canonical_ensemble enhanced-sampling by agrossfield on 2009-10-30 19:23:37 as
	Observation of buried water molecules in phospholipid membranes by surface sum-frequency generation spectroscopy [My Copy] The Journal of Chemical Physics, Vol. 131, No. 16. (2009), 161107. by Maria Sovago, Erik Vartiainen, Mischa Bonn posted to water membrane-electrostatics by agrossfield on 2009-10-30 19:22:35 as along with 1 person cjryan
	Error and efficiency of replica exchange molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 131, No. 16. (2009), 165102. by Edina Rosta, Gerhard Hummer posted to replica-exchange by agrossfield on 2009-10-30 19:21:06 as
	Coarse-Grained Protein Model with Residue Orientation Energies Derived from Atomic Force Fields [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 44. (5 November 2009), pp. 14824-14830. by Marcos R. Betancourt posted to coarse-grain by agrossfield on 2009-10-30 03:02:32 as
	Simulation of the effects of chain architecture on the sorption of ethylene in polyethylene [My Copy] The Journal of Chemical Physics, Vol. 120, No. 23. (2004), pp. 11304-11315. by Brian J. Banaszak, Roland Faller, Juan J. de Pablo posted to replica-exchange by agrossfield on 2009-10-26 19:18:59 as
	Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 3. (2009), 031911. by Igor S. Tolokh, Victor Vivcharuk, Bruno Tomberli, C. G. Gray posted to free-energy antimicrobial-peptide by agrossfield on 2009-10-23 17:16:16 as
	Structural imperatives impose diverse evolutionary constraints on helical membrane proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 42. (20 October 2009), pp. 17747-17750. by Amit Oberai, Nathan H. Joh, Frank K. Pettit, James U. Bowie posted to membrane-proteins by agrossfield on 2009-10-22 15:00:19 as
	Structure of the Amyloid-β (1−42) Monomer Absorbed To Model Phospholipid Bilayers: A Molecular Dynamics Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 43. (29 October 2009), pp. 14480-14486. by Charles H. Davis, Max L. Berkowitz posted to lipid-protein-interactions amyloid by agrossfield on 2009-10-22 14:58:36 as
	Spectral distortion effects due to finite pulse widths in deuterium nuclear magnetic resonance spectroscopy [My Copy] Can. J. Phys., Vol. 58, No. 10. (1980), pp. 1510-1517. by Myer Bloom, James H. Davis, Marko I. Valic posted to nmr by agrossfield on 2009-10-20 01:53:42 as
	Wormlike Micelle Formation in Peptide-Lipid Conjugates Driven by Secondary Structure Transformation of the Headgroups† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 42. (22 October 2009), pp. 13711-13714. by Tomoko Shimada, Sangwoo Lee, Frank S. Bates, Atsushi Hotta, Matthew Tirrell posted to lipopeptide by agrossfield on 2009-10-15 18:43:36 as
	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
	General Theoretical/Computational Tool for Interpreting NMR Spin Relaxation in Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 41. (15 October 2009), pp. 13613-13625. by Mirco Zerbetto, Antonino Polimeno, Eva Meirovitch posted to nmr by agrossfield on 2009-10-08 21:28:04 as along with 1 person francescamocci
	Coarse-Grained Molecular Dynamics Simulation of the Aggregation Properties of Multiheaded Cationic Surfactants in Water [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 41. (15 October 2009), pp. 13545-13550. by Suman K. Samanta, Santanu Bhattacharya, Prabal K. Maiti posted to coarse-grain antimicrobial-peptide by agrossfield on 2009-10-08 15:52:12 as
	Generalized Langevin models of molecular dynamics simulations with applications to ion channels [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134102. by Dan Gordon, Vikram Krishnamurthy, Shin H. Chung posted to langevin ion-channel free-energy by agrossfield on 2009-10-07 20:57:15 as along with 1 person dlimmer
	Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134110. by David D. L. Minh, John D. Chodera posted to free-energy by agrossfield on 2009-10-07 20:55:44 as along with 1 person dlimmer
	Structure and Dynamics of Membrane Proteins by Magic Angle Spinning Solid-State NMR [My Copy] Annual Review of Biophysics, Vol. 38, No. 1. (2009), pp. 385-403. by Ann McDermott posted to nmr by agrossfield on 2009-10-06 21:31:04 as along with 4 people andreasauerwein leocmcheung zwang viktor21614
	Comparative Study of Two Plasticins: Specificity, Interfacial Behavior, and Bactericidal Activity [My Copy] Biochemistry, Vol. 48, No. 40. (13 October 2009), pp. 9372-9383. by Pierre Joanne, Mélanie Falord, Olivier Chesneau, et al.Claire Lacombe, Sabine Castano, Bernard Desbat, Constance Auvynet, Pierre Nicolas, Tarek Msadek, Chahrazade El Amri posted to antimicrobial-peptide by agrossfield on 2009-10-06 15:15:01 as along with 1 person qshao
	Structural waters define a functional channel mediating activation of the GPCR, rhodopsin [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 34. (2009), pp. 14367-14372. by Thomas E. Angel, Sayan Gupta, Beata Jastrzebska, Krzysztof Palczewski, Mark R. Chance posted to rhodopsin internal-water gpcr by agrossfield on 2009-10-05 17:29:17 as
	Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13279-13290. by In S. Joung, Thomas E. Cheatham posted to ion-solvation by agrossfield on 2009-10-01 18:54:15 as along with 1 person qshao
	Molecular Dynamics Simulation Study of Correlated Motions in Phospholipid Bilayer Membranes [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13229-13234. by Matthew Roark, Scott E. Feller posted to membrane by agrossfield on 2009-10-01 18:53:14 as along with 2 people sobolevnrm dimka
	Membrane structure and conformational changes of the antibiotic heterodimeric peptide distinctin by solid-state NMR spectroscopy [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 39. (29 September 2009), pp. 16639-16644. by Jarbas M. Resende, ClÃ©ria M. Moraes, Victor H. O. Munhoz, et al.Christopher Aisenbrey, Rodrigo M. Verly, Philippe Bertani, Amary Cesar, Dorila PilÃ³-Veloso, Burkhard Bechinger posted to nmr antimicrobial-peptide by agrossfield on 2009-09-30 14:52:35 as along with 1 person paulschlesinger
	Order of lipid phases in model and plasma membranes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 39. (29 September 2009), pp. 16645-16650. by Hermann-Josef Kaiser, Daniel Lingwood, Ilya Levental, et al.Julio L. Sampaio, Lucie Kalvodova, Lawrence Rajendran, Kai Simons posted to rafts by agrossfield on 2009-09-30 14:51:09 as along with 1 person paulschlesinger
	Molecular-Level Organization of Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol† [My Copy] Biochemistry, Vol. 43, No. 49. (1 December 2004), pp. 15318-15328. by Michael C. Pitman, Frank Suits, Alexander D. MacKerell, Scott E. Feller posted to rafts polyunsaturated_fatty_acids nmr by agrossfield on 2009-09-29 12:34:03 as
	Role of Short-Range Directional Interactions in Coarse-Graining of Protic/Aprotic Liquids [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 39. (1 October 2009), pp. 12988-12998. by Piotr Kowalczyk, Piotr A. Gauden, Alina Ciach posted to coarse-grain by agrossfield on 2009-09-25 17:51:06 as
	Transition path sampling of water exchange rates and mechanisms around aqueous ions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 11. (2009), 114512. by Sebastien Kerisit, Kevin M. Rosso posted to ion-solvation by agrossfield on 2009-09-22 16:35:34 as along with 1 person dlimmer
	Experimental approaches to membrane thermodynamics [My Copy] Soft Matter, Vol. 5, No. 17. (2009), pp. 3249-3257. by Peter Westh posted to membrane by agrossfield on 2009-09-21 17:46:26 as along with 3 people cjryan flbarroso sobolevnrm
	Effects of induced tension and electrostatic interactions on the mechanisms of antimicrobial peptide translocation across lipid bilayer [My Copy] Soft Matter, Vol. 5, No. 17. (2009), pp. 3312-3318. by Lianghui Gao, Weihai Fang posted to antimicrobial-peptide by agrossfield on 2009-09-21 17:44:39 as along with 1 person flbarroso
	Cation specific binding with protein surface charges [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 32. (2009), pp. 13296-13300. by Berk Hess, Nico F. A. van der Vegt posted to ion-solvation by agrossfield on 2009-09-21 17:43:33 as
	A Combined Pulse EPR and Monte Carlo Simulation Study Provides Molecular Insight on Peptide−Membrane Interactions [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 38. (24 September 2009), pp. 12687-12695. by Michal Gordon-Grossman, Yana Gofman, Herbert Zimmermann, et al.Veronica Frydman, Yechiel Shai, Nir Ben-Tal, Daniella Goldfarb posted to antimicrobial-peptide by agrossfield on 2009-09-19 20:42:33 as
	Extracting the Causality of Correlated Motions from Molecular Dynamics Simulations [My Copy] Vol. 97, No. 6. (16 September 2009), pp. 1747-1755. by Hiqmet Kamberaj, Arjan van der Vaart posted to pca by agrossfield on 2009-09-15 21:44:19 as along with 1 person oteri
	Extended ensemble approach for deriving transferable coarse-grained potentials [My Copy] The Journal of Chemical Physics, Vol. 131, No. 10. (2009), 104110. by J. W. Mullinax, W. G. Noid posted to coarse-grain by agrossfield on 2009-09-15 13:10:10 as
	Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 10. (2009), 104102. by Uwe Winter, Tihamér Geyer posted to integrator coarse-grain by agrossfield on 2009-09-15 13:09:33 as along with 3 people and 1 group dlimmer whitead paulschlesinger Jiang Research Group
	Advanced multiple time scale molecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 131, No. 10. (2009), 104101. by Igor P. Omelyan posted to multiple-time-step by agrossfield on 2009-09-15 13:08:08 as along with 1 person dlimmer
	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 molecular_dynamics_simulations gpcr by agrossfield on 2009-09-11 13:56:35 as along with 11 people and 1 group xdeupi allmensch bmduggan r2s2 apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Theory of Free Energy and Entropy in Noncovalent Binding [My Copy] Chemical Reviews, Vol. 109, No. 9. (9 September 2009), pp. 4092-4107. by Huan-Xiang Zhou, Michael K. Gilson posted to ligand-binding by agrossfield on 2009-09-10 14:49:19 as along with 6 people and 1 group cchang anuragsethi sobolevnrm dr_proton qshao paulschlesinger Chang group
	Structure of the BK potassium channel in a lipid membrane from electron cryomicroscopy. [My Copy] Nature, Vol. 461, No. 7261. (10 September 2009), pp. 292-295. by Liguo Wang, Fred J. Sigworth posted to potassium_channel cryomicroscopy by agrossfield on 2009-09-10 02:28:18 as along with 2 people faion paulschlesinger
	On the fluctuations that drive small ions toward, and away from, interfaces between polar liquids and their vapors [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 36. (8 September 2009), pp. 15125-15130. by Joyce Noah-Vanhoucke, Phillip L. Geissler posted to ions ion-solvation by agrossfield on 2009-09-09 18:38:59 as
	Recent advances in solid-state NMR spectroscopy of spin I = 1/2 nuclei [My Copy] Physical Chemistry Chemical Physics, Vol. 11, No. 32. (2009), pp. 6876-6891. by Anne Lesage posted to nmr_spectroscopy nmr by agrossfield on 2009-09-08 20:03:54 as
	Estimating the sampling error: Distribution of transition matrices and functions of transition matrices for given trajectory data [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 2. (2009), 021106. by Philipp Metzner, Frank Noé, Christof Schütte posted to markov error_distribution error-analysis by agrossfield on 2009-09-08 20:02:15 as
	Application of the fuzzy-oil-drop model to membrane protein simulation [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77 (2009), pp. 378-394. by Veronica Zobnina, Irena Roterman posted to implicit-membrane by agrossfield on 2009-09-07 12:55:07 as
	Aggregation of Transmembrane Peptides Studied by Spin-Label EPR [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 36. (10 September 2009), pp. 12257-12264. by Francesco Scarpelli, Malte Drescher, Tania Rutters-Meijneke, et al.Andrea Holt, Dirk T. S. Rijkers, J. Antoinette Killian, Martina Huber posted to walp antimicrobial-peptide by agrossfield on 2009-09-06 18:43:16 as
	Molecular Interactions between Magainin 2 and Model Membranes in Situ [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 36. (10 September 2009), pp. 12358-12363. by Khoi T. Nguyen, Stéphanie V. Le Clair, Shuji Ye, Zhan Chen posted to magainin by agrossfield on 2009-09-06 18:42:43 as
	Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 9. (2009), 094107. by V. Ballenegger, A. Arnold, J. J. Cerdà posted to electrostatics by agrossfield on 2009-09-05 15:50:03 as
	Theoretically informed coarse grain simulations of polymeric systems [My Copy] The Journal of Chemical Physics, Vol. 131, No. 8. (2009), 084903. by Darin Q. Pike, François A. Detcheverry, Marcus Müller, Juan J. de Pablo posted to field-theory coarse-grain by agrossfield on 2009-08-31 21:42:44 as
	Permeability of Small Molecules through a Lipid Bilayer: A Multiscale Simulation Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 35. (3 September 2009), pp. 12019-12029. by Mario Orsi, Wendy E. Sanderson, Jonathan W. Essex posted to gay-berne coarse-grain by agrossfield on 2009-08-28 15:57:25 as along with 1 person sobolevnrm
	Antibiotics for Emerging Pathogens [My Copy] Science, Vol. 325, No. 5944. (28 August 2009), pp. 1089-1093. by Michael A. Fischbach, Christopher T. Walsh posted to drug-development antibiotic-resistance by agrossfield on 2009-08-28 15:54:31 as along with 1 person dbikard

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antimicrobial-peptide	80
coarse-grain	50
free-energy	26
membrane	23
ion-solvation	21
lipid-protein-interactions	19
nmr	19
rhodopsin	17
implicit-membrane	16
membrane-electrostatics	16
gpcr	15
membrane-proteins	15
pca	14
lipopeptide	11
replica-exchange	11
rafts	10
implicit-solvent	8
membrane-forcefield	8
network-model	8
protein-folding	7
ion-channel	6
jarzynski	6
b2ar	5
forcefield	5
internal-water	5
electrostatics	4
ligand-binding	4
lipid-curvature	4
me	4
pepducin	4
pmf	4
scattering	4
waxs	4
wham	4
alamethicin	3
amyloid	3
defensin	3
integrator	3
langevin	3
membrane-fusion	3
membrane-theory	3
phosphorus	3
thermostats	3
bacteriorhodopsin	2
beta-adrenergic	2
cholesterol	2
convergence	2
dpd	2
enhanced-sampling	2
error-analysis	2
glycophorin	2
isotropic-periodic-sum	2
lattice	2
magainin	2
md	2
multiscale	2
path-sampling	2
polarizability	2
protegrin	2
protein-hydration	2
solvation	2
water	2
allostery	1
antibiotic-resistance	1
barrel-stave	1
bicelles	1
cecropin	1
charge	1
clustering	1
colicin	1
crowding	1
cryomicroscopy	1
demixing	1
dendrite	1
detergent	1
dipole-lattice	1
drug-development	1
error_distribution	1
ewald	1
fabp	1
field-theory	1
finite-size-effect	1
fission	1
flip-flop	1
flu	1
fluoresence	1
fluorination	1
gay-berne	1
generalized-born	1
grand_canonical_ensemble	1
helfrich	1
hemagglutinin	1
hiv	1
hiv_virus	1
hydrophobicity-scale	1
hydrophobic-mismatch	1
inherent-structure	1
ions	1
lambda-dynamics	1
markov	1
methods	1
modeling-software	1
molecular_dynamics_simulations	1
multiple-time-step	1
nanotube	1
nmr_spectroscopy	1
osmolytes	1
pengyu	1
peptide	1
polymer	1
polyunsaturated_fatty_acids	1
pores	1
porin	1
potassium_channel	1
pressure-profile	1
ras	1
rigid-body	1
salt	1
sevi	1
shaw	1
simulation	1
src	1
steered-md	1
structure	1
structure-prediction	1
superposition	1
umbrella-sampling	1
unsaturated	1
vesicles	1
walp	1

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