Group: baker-group - with tag molecular_simulation [at least 200 articles] Export

Recent papers posted by members of the baker-group group with tag molecular_simulation

	Salt induced asymmetry in membrane simulations by partial restriction of ionic motion. [My Copy] The Journal of chemical physics, Vol. 130, No. 19. (21 May 2009) by Fernando E E. Herrera, Sergio Pantano posted to biomembranes electrostatics molecular_simulation by sobolevnrm to the group baker-group on 2009-05-27 12:02:13 as
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2009-05-19 12:00:47 as along with 8 people rodrigofaccioli mmuecke medic0747 flbarroso jrperillaj xavierprat saravan dimka
	Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis [My Copy] PLoS ONE, Vol. 4, No. 5. (13 May 2009), e5525. by Nilesh K. Banavali, Alexander D. Mackerell posted to free_energy molecular_simulation nucleic_acids by sobolevnrm to the group baker-group on 2009-05-13 12:12:15 as along with 1 person and 1 group barry McCammon
	Reproducing Basic pKa Values for Turkey Ovomucoid Third Domain Using a Polarizable Force Field [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Timothy H. Click, George A. Kaminski posted to electrostatics molecular_simulation pka solvation by sobolevnrm to the group baker-group on 2009-05-13 12:10:31 as
	Explicitly Representing the Solvation Shell in Continuum Solvent Calculations [My Copy] The Journal of Physical Chemistry A, Vol. 0, No. 0. (0000) by Eirik F. da Silva, Hallvard F. Svendsen, Kenneth M. Merz posted to electrostatics molecular_simulation multiscale quantum_mechanics solvation by sobolevnrm to the group baker-group on 2009-05-11 12:27:40 as along with 2 people goncalojustino carlosjavierna
	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 enhanced_sampling molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-04-23 12:32:31 as along with 2 people bmduggan paulschlesinger
	Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 47, No. 3. (2002), pp. 393-402. by Elmar Krieger, Günther Koraimann, Gert Vriend posted to molecular_simulation optimization structure_prediction by sobolevnrm to the group baker-group on 2009-04-23 12:29:22 as
	Molecular dynamics simulations of membrane channels and transporters [My Copy] Current Opinion in Structural Biology (01 April 2009) by Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad Tajkhorshid, Klaus Schulten posted to biomembranes ion_channels molecular_simulation review by sobolevnrm to the group baker-group on 2009-04-21 12:30:01 as along with 2 people dimka paulschlesinger
	Models for Phosphatidylglycerol Lipids Put to a Structural Test [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Jérôme Hénin, Wataru Shinoda, Michael L. Klein posted to biomembranes molecular_simulation by sobolevnrm to the group baker-group on 2009-04-20 12:35:36 as along with 1 person agrossfield
	Green-Function-Based Monte Carlo Method for Classical Fields Coupled to Fermions [My Copy] Physical Review Letters, Vol. 102, No. 15. (2009), 150604. by Alexander posted to beyond_mean_field molecular_simulation statistical_mechanics by sobolevnrm to the group baker-group on 2009-04-20 12:34:04 as
	Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 5. (12 May 2009), pp. 1393-1399. by Edina Rosta, Nicolae-Viorel Buchete, Gerhard Hummer posted to free_energy molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2009-04-16 12:35:09 as
	On the Range of Water Structure Models Compatible with X-ray and Neutron Diffraction Data [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 18. (7 May 2009), pp. 6246-6255. by Kjartan T. Wikfeldt, Mikael Leetmaa, Mathias P. Ljungberg, Anders Nilsson, Lars G. M. Pettersson posted to experimental_methodology molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-04-16 12:34:32 as along with 3 people qshao willard flbarroso
	Polarizable Ions at Interfaces [My Copy] Physical Review Letters, Vol. 102, No. 14. (2009), 147803. by Yan Levin posted to electrostatics free_energy molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-04-15 12:13:00 as along with 1 person agrossfield
	Simulated x-ray scattering of protein solutions using explicit-solvent models [My Copy] The Journal of Chemical Physics, Vol. 130, No. 13. (2009), 134114. by Sanghyun Park, Jaydeep P. Bardhan, Benoît Roux, Lee Makowski posted to molecular_simulation protein-protein_interactions solvation by sobolevnrm to the group baker-group on 2009-04-15 12:12:10 as along with 1 person agrossfield
	Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Richard M. Venable, Linda E. Chen, Richard W. Pastor posted to biomembranes electrostatics interfaces molecular_simulation by sobolevnrm to the group baker-group on 2009-04-15 12:11:12 as along with 1 person agrossfield
	Sampling conformations in high dimensions using low-dimensional distribution functions [My Copy] The Journal of Chemical Physics, Vol. 130, No. 13. (2009), 134102. by Sandeep Somani, Benjamin J. Killian, Michael K. Gilson posted to enhanced_sampling free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-04-03 12:49:33 as along with 1 person VGreiff
	Monte Carlo Simulations of Salt Solutions: Exploring the Validity of Primitive Models [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Zareen Abbas, Elisabet Ahlberg, Sture Nordholm posted to electrostatics molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-04-03 12:49:19 as
	Computational studies of aqueous interfaces of RbBr salt solutions [My Copy] The Journal of Chemical Physics, Vol. 130, No. 12. (2009), 124709. by Xiuquan Sun, Liem X. Dang posted to electrostatics molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-03-28 16:15:58 as
	Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Morgan Lawrenz, Riccardo Baron, Andrew J. Mccammon posted to free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-03-28 16:15:48 as
	Rational design of ion force fields based on thermodynamic solvation properties [My Copy] The Journal of Chemical Physics, Vol. 130, No. 12. (2009), 124507. by Dominik Horinek, Shavkat I. Mamatkulov, Roland R. Netz posted to electrostatics molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-03-28 16:15:23 as along with 1 person mikaellund
	Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Devleena Shivakumar, Yuqing Deng, Benoît Roux posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-28 16:14:50 as along with 4 people pachulito carlosjavierna pmk ibuch
	Structural properties of polymeric DNA from molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 130, No. 11. (2009), 115103. by Sudipta Samanta, Supti Mukherjee, Jaydeb Chakrabarti, Dhananjay Bhattacharyya posted to mechanics molecular_simulation nucleic_acids solvation by sobolevnrm to the group baker-group on 2009-03-27 11:57:56 as
	Grand Canonical Free-Energy Calculations of Protein−Ligand Binding [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Matthew Clark, Sia Meshkat, Jeffrey S. Wiseman posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-27 11:57:25 as
	Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Robert V. Swift, Andrew J. Mccammon posted to allostery molecular_simulation by sobolevnrm to the group baker-group on 2009-03-27 11:56:40 as along with 1 person jrperillaj
	Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (20 March 2009), e1000323. by Giulia Morra, Gennady Verkhivker, Giorgio Colombo posted to allostery molecular_simulation by sobolevnrm to the group baker-group on 2009-03-27 11:56:09 as along with 1 person and 1 group barry McCammon
	Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization [My Copy] The Journal of Chemical Physics, Vol. 130, No. 11. (2009), 115102. by Li L. Duan, Ye Mei, Qing G. Zhang, John Z. H. Zhang posted to electrostatics molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-03-26 11:37:32 as
	Molecular dynamics simulation of a mixed lipid emulsion model: Influence of the triglycerides on interfacial phospholipid organization [My Copy] Journal of Molecular Structure: THEOCHEM (26 January 2009) by Gaëlle Henneré, Patrice Prognon, Françoise Brion, Véronique Rosilio, Ioannis Nicolis posted to biomembranes emulsions molecular_simulation by sobolevnrm to the group baker-group on 2009-03-26 11:36:22 as along with 1 person paulschlesinger
	Path-Integral Method for Predicting Relative Binding Affinities of Protein−Ligand Complexes [My Copy] Journal of the American Chemical Society, Vol. 131, No. 12. (1 April 2009), pp. 4521-4528. by Chandrika Mulakala, Yiannis N. Kaznessis posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-26 11:33:09 as along with 1 person carlosjavierna
	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, Vol. 106, No. 10. (10 March 2009), pp. 3776-3781. by Sichun Yang, Nilesh K. Banavali, BenoÃ®t Roux posted to allostery enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2009-03-26 11:32:54 as along with 7 people and 1 group anuragsethi Diego_Prada bmduggan allmensch guhjy barry jmccammon McCammon
	Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Slimane Doudou, Neil A. Burton, Richard H. Henchman posted to free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-03-26 11:32:09 as along with 4 people and 2 groups jmccammon A_Coletta_Thesis carlosjavierna ibuch McCammon Structural Biology Group TorVergata
	Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations† [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by David L. Mobley, Christopher I. Bayly, Matthew D. Cooper, Ken A. Dill posted to electrostatics molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-03-25 11:38:16 as along with 3 people and 1 group ucbcjbm willard whitead Jiang Research Group
	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 molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2009-03-25 11:37:45 as along with 3 people and 1 group bmduggan oteri mleis Structural Biology Group TorVergata
	Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic integration data [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2297-2304. by Conrad Shyu, F. Marty Ytreberg posted to free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-03-25 11:36:22 as
	Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach [My Copy] The Journal of Chemical Physics, Vol. 130, No. 8. (2009), 084107. by A. Ghysels, D. Van Neck, B. R. Brooks, V. Van Speybroeck, M. Waroquier posted to molecular_simulation quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-25 11:31:29 as along with 1 person barry
	Nitric oxide reactivity with globins as investigated through computer simulation. [My Copy] Methods in enzymology, Vol. 437 (2008), pp. 477-498. by M. A. Marti, L. Capece, A. Bidon-Chanal, et al.A. Crespo, V. Guallar, F. J. Luque, D. A. Estrin posted to molecular_simulation nitric_oxide by sobolevnrm to the group baker-group on 2009-03-25 11:31:16 as along with 1 person onufriev
	Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (20 February 2009), e1000293. by Michael D. Daily, Jeffrey J. Gray posted to allostery molecular_simulation by sobolevnrm to the group baker-group on 2009-03-24 12:22:46 as along with 9 people and 2 groups anuragsethi skywalkerus02 pablocarb AngelB eallain allmensch gane5h apaydin barry structural_bioinformatics McCammon
	Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Adrian P. Wiley, Sarah L. Williams, Jonathan W. Essex posted to clustering molecular_simulation quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-23 11:51:27 as
	Gaussian-Mixture Umbrella Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Paul Maragakis, Arjan van der Vaart, Martin Karplus posted to enhanced_sampling free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-03-23 11:51:09 as along with 2 people willard agrossfield
	Effective force coarse-graining [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 12. (2009), pp. 2002-2015. by Yanting Wang, W. G. Noid, Pu Liu, Gregory A. Voth posted to molecular_simulation multiscale by sobolevnrm to the group baker-group on 2009-03-23 11:50:49 as along with 3 people and 1 group jmccammon mbeeby flbarroso McCammon
	Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 19. (14 May 2009), pp. 6782-6791. by Christopher J. Fennell, Alan Bizjak, Vojko Vlachy, Ken A. Dill posted to electrostatics molecular_simulation solvation by sobolevnrm to the group baker-group on 2009-03-22 14:04:35 as along with 2 people flbarroso mikaellund
	An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 9. (5 March 2009), pp. 2748-2763. by See-Wing Chiu, Sagar A. Pandit, H. L. Scott, Eric Jakobsson posted to biomembranes molecular_simulation by sobolevnrm to the group baker-group on 2009-03-22 14:03:02 as along with 1 person loison
	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 molecular_dynamics molecular_simulation programming software visualization by sobolevnrm to the group baker-group on 2009-03-20 11:47:34 as along with 10 people and 2 groups anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque ruvido massivemayhem barry RamuAnandakrishnan structural_bioinformatics McCammon
	Improved United-Atom Models for Perfluorinated Self-Assembled Monolayers [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 8. (26 February 2009), pp. 3300-3312. by J. J. Nogueira, E. Martínez-Núñez, S. A. Vázquez posted to biomembranes molecular_simulation by sobolevnrm to the group baker-group on 2009-03-20 11:46:01 as
	SHARPEN-Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network. [My Copy] Journal of computational chemistry (23 January 2009) by Ilya V V. Loksha, James R R. Maiolo, Cheng W W. Hong, Albert Ng, Christopher D D. Snow posted to enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2009-03-19 12:07:42 as along with 3 people and 2 groups apaydin A_Coletta_Thesis barry Structural Biology Group TorVergata structural_bioinformatics
	Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models. [My Copy] Biophysical journal, Vol. 96, No. 2. (January 2009), pp. 385-402. by J. E. Davis, O. Rahaman, S. Patel posted to biomembranes molecular_simulation by sobolevnrm to the group baker-group on 2009-03-18 11:28:34 as
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-18 11:23:06 as along with 9 people and 1 group anuragsethi flbarroso mikaellund barry jmccammon willard agrossfield carlosjavierna ibuch McCammon
	Similarity Measures for Protein Ensembles [My Copy] PLoS ONE, Vol. 4, No. 1. (15 January 2009), e4203. by Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg posted to bioinformatics clustering molecular_simulation quasiharmonic_models structure by sobolevnrm to the group baker-group on 2009-03-18 11:22:13 as along with 8 people and 2 groups anuragsethi klexa apaydin gane5h barry jmccammon reyez biehl structural_bioinformatics McCammon
	Molecular simulation with variable protonation states at constant pH [My Copy] The Journal of Chemical Physics, Vol. 126, No. 16. (2007), 164112. by Harry A. Stern posted to electrostatics molecular_simulation pka solvation by sobolevnrm to the group baker-group on 2009-03-16 11:52:57 as
	Renormalization Group by Monte Carlo Methods [My Copy] Physical Review Letters, Vol. 37, No. 8. (1976), 461. by Shang-Keng Ma posted to molecular_simulation review statistical_mechanics by sobolevnrm to the group baker-group on 2009-03-13 11:24:43 as
	ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. [My Copy] Journal of computational chemistry, Vol. 30, No. 5. (15 April 2009), pp. 673-699. by A. Vitalis, R. V. Pappu posted to electrostatics molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2009-03-05 12:34:48 as along with 2 people melo_mcr agrossfield

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solvation	136
electrostatics	122
molecular_dynamics	111
biomembranes	88
multiscale	52
enhanced_sampling	38
allostery	32
free_energy	32
quasiharmonic_models	23
nucleic_acids	22
protein-ligand_interactions	16
statistical_mechanics	15
adsorption	14
zeolite	14
mathematics	13
protein_folding	12
quasiharmonic-models_elastic-network_gnm_nma_pca_etc	11
interfaces	10
nonpolar	10
review	10
diffusion	9
software	9
experimental_methodology	8
quantum_mechanics	8
structure	8
fluid_dynamics	7
microfluidics	7
clustering	6
ion_channels	6
kinetics	6
protein-membrane_interactions	6
protein-protein_interactions	6
bioinformatics	5
nanotech	5
beyond_mean_field	4
metalloregulation	4
monte_carlo	4
perfluorocarbons	4
pka	4
teaching	4
visualization	4
materials_studio	3
model_building	3
nucleic_acid_builder	3
oct09	3
ribosome	3
sterols	3
correlated_mutations	2
correlations	2
cytoskeleton	2
docking	2
drug_design	2
emulsions	2
generalized_born	2
ligand-membrane_interactions	2
mechanics	2
misc	2
networks	2
nitric_oxide	2
nmr	2
nmr_measurements	2
optimization	2
programming	2
protein-nucleic_acid_interactions	2
statistics	2
structure_prediction	2
thrombin	2
biomembrane	1
coarse-grained	1
elastic	1
intermolecular	1
nanoparticles	1
network	1
sabio	1
simulation	1

Group: baker-group - with tag molecular_simulation [at least 200 articles] Export

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