sobolevnrm's Pande:VS [42 articles] Export

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	Bayesian Detection of Intensity Changes in Single Molecule and Molecular Dynamics Trajectories [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Daniel L. Ensign, Vijay S. Pande posted to statistics molecular_dynamics by sobolevnrm on 2009-12-20 14:15:04 as along with 1 person and 1 group samjlord moernerlab
	Progress and challenges in the automated construction of Markov state models for full protein systems [My Copy] J. Chem. Phys., Vol. 131, No. 12. (Sep 2009) by Gregory R. Bowman, Kyle A. Beauchamp, George Boxer, Vijay S. Pande posted to statistics molecular-dynamics kinetics diffusion by sobolevnrm on 2009-10-31 21:00:31 as
	Bayesian Single-Exponential Kinetics in Single-Molecule Experiments and Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 36. (10 September 2009), pp. 12410-12423. by Daniel L. Ensign, Vijay S. Pande posted to molecular_dynamics mathematics kinetics by sobolevnrm on 2009-10-16 13:42:25 as along with 2 people and 1 group paulymer samjlord moernerlab
	PAPER - Accelerating parallel evaluations of ROCS [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Imran S. Haque, Vijay S. Pande posted to docking programming protein-ligand_interactions by sobolevnrm on 2009-05-07 13:00:11 as along with 1 person and 1 group ihaque baker-group
	Topological methods for exploring low-density states in biomolecular folding pathways [My Copy] The Journal of Chemical Physics, Vol. 130, No. 14. (2009), 144115. by Yuan Yao, Jian Sun, Xuhui Huang, et al.Gregory R. Bowman, Gurjeet Singh, Michael Lesnick, Leonidas J. Guibas, Vijay S. Pande, Gunnar Carlsson posted to clustering energy_landscapes nucleic_acids protein_folding by sobolevnrm on 2009-04-17 13:03:38 as along with 1 group baker-group
	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 on 2009-03-20 11:47:34 as along with 11 people and 3 groups oteri anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque ruvido massivemayhem barry RamuAnandakrishnan baker-group structural_bioinformatics McCammon
	Side-chain recognition and gating in the ribosome exit tunnel [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 43. (28 October 2008), pp. 16549-16554. by Paula M. Petrone, Christopher D. Snow, Del Lucent, Vijay S. Pande posted to molecular_simulation ribosome by sobolevnrm on 2009-02-04 12:36:05 as along with 2 people and 2 groups carlosjavierna barry baker-group McCammon
	Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble [My Copy] Journal of the American Chemical Society, Vol. 130, No. 37. (2008), 12334-12341. by Yu Bai, Vincent B. Chu, Jan Lipfert, Vijay S. Pande, Daniel Herschlag, Sebastian Doniach posted to electrostatics solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:10 as
	Chemical Denaturants Inhibit the Onset of Dewetting [My Copy] Journal of the American Chemical Society, Vol. 130, No. 36. (2008), pp. 11854-11855. by Jeremy L. England, Vijay S. Pande, Gilad Haran posted to solvation by sobolevnrm on 2008-10-10 12:13:27 as
	Normal mode partitioning of Langevin dynamics for biomolecules [My Copy] The Journal of Chemical Physics, Vol. 128, No. 14. (2008) by Christopher R. Sweet, Paula Petrone, Vijay S. Pande, Jesús A. Izaguirre posted to molecular_dynamics multiscale quasiharmonic_models by sobolevnrm on 2008-05-12 11:53:54 as along with 2 people and 1 group paulschlesinger aqeel baker-group
	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 enhanced_sampling molecular_simulation by sobolevnrm on 2008-04-03 12:01:58 as along with 2 people and 1 group bmduggan arnaucordomi baker-group
	Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry [My Copy] J. Med. Chem. (24 January 2008) by Anthony Nicholls, David L. Mobley, Peter J. Guthrie, John D. Chodera, Vijay S. Pande posted to electrostatics nonpolar solvation by sobolevnrm on 2008-03-26 11:40:27 as along with 2 people and 1 group dmobley middledomain baker-group
	Theory for an order-driven disruption of the liquid state in water [My Copy] The Journal of Chemical Physics, Vol. 128, No. 4. (2008) by Jeremy L. England, Sanghyun Park, Vijay S. Pande posted to molecular_dynamics solvation by sobolevnrm on 2008-02-29 12:20:30 as along with 1 person and 1 group dmobley baker-group
	Solvent Viscosity Dependence of the Protein Folding Dynamics [My Copy] J. Phys. Chem. B (30 January 2008) by Y. M. Rhee, V. S. Pande posted to kinetics molecular_simulation protein_folding solvation by sobolevnrm on 2008-02-27 12:33:44 as along with 1 person and 1 group paulymer baker-group
	Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e220. by Peter M. Kasson, Vijay S. Pande posted to biomembranes molecular_dynamics molecular_simulation by sobolevnrm on 2008-01-03 12:34:07 as along with 3 people and 1 group zwang paulschlesinger Ema baker-group
	Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e220. by Peter M. Kasson, Vijay S. Pande posted to biomembranes molecular_simulation by sobolevnrm on 2007-12-27 12:45:22 as along with 2 people and 1 group cjryan Ema baker-group
	Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics [My Copy] PLoS Computational Biology, Vol. preprint, No. 2007. (1 September 2007), e220.eor. by Peter Kasson, Vijay S. Pande posted to biomembranes molecular_dynamics by sobolevnrm on 2007-12-11 17:41:03 as along with 1 group baker-group
	Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations [My Copy] J. Phys. Chem. B (19 October 2007) by M. R. Shirts, D. L. Mobley, J. D. Chodera, V. S. Pande posted to molecular_dynamics molecular_simulation nonpolar solvation by sobolevnrm on 2007-11-06 12:41:10 as along with 1 group baker-group
	Effects of long-range electrostatic forces on simulated protein folding kinetics [My Copy] Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 694-700. by Alex Robertson, Edgar Luttmann, Vijay S. Pande posted to electrostatics molecular_simulation protein_folding by sobolevnrm on 2007-09-14 12:41:24 as along with 2 people and 1 group r2s2 RamuAnandakrishnan baker-group
	Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics [My Copy] Journal of Chemical Physics, Vol. 126 (2007) by N. S. Hinrichs, V. S. Pande posted to kinetics molecular_dynamics by sobolevnrm on 2007-07-07 23:53:48 as along with 1 group baker-group
	Protein folding under confinement: A role for solvent [My Copy] Proceedings of the National Academy of Sciences of the United States of America (in press) by D. Lucent, V. Vishal, V. S. Pande posted to protein_folding solvation by sobolevnrm on 2007-06-18 13:08:48 as along with 1 group baker-group
	Persistent voids: a new structural metric for membrane fusion [My Copy] Bioinformatics (in press) by P. M. Kasson, A. Zomorodian, S. Park, N. Singhals, L. J. Guibas, V. S. Pande posted to biomembranes molecular_simulation by sobolevnrm on 2007-05-25 14:38:05 as along with 1 group baker-group
	Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics [My Copy] Journal of Chemical Physics, Vol. 126 (2007) by J. D. Chodera, N. Singhal, V. S. Pande, K. A. Dill, W. C. Swope posted to molecular_dynamics protein_folding quasiharmonic_models by sobolevnrm on 2007-05-25 14:37:07 as along with 1 group baker-group
	Bayesian update method for adaptive weighted sampling [My Copy] Physical Review E, Vol. 74 (2006) by S. Park, D. L. Ensign, V. S. Pande posted to mathematics quasiharmonic_models by sobolevnrm on 2007-05-25 14:36:04 as along with 1 group baker-group
	Error analysis and efficient sampling in Markovian state models for molecular dynamics [My Copy] Journal of Chemical Physics, Vol. 123 (2005) by N. Singhal, V. S. Pande posted to diffusion molecular_dynamics statistical_mechanics by sobolevnrm on 2007-05-25 14:23:18 as along with 1 group baker-group
	Validation of Markov state models using Shannon's entropy [My Copy] Journal of Chemical Physics, Vol. 124 (2006) by S. Park, V. S. Pande posted to diffusion statistical_mechanics by sobolevnrm on 2007-05-25 14:23:18 as along with 1 group baker-group
	One-Dimensional Reaction Coordinate and the Corresponding Potential of Mean Force from Commitment Probability Distribution [My Copy] Journal of Physical Chemistry B, Vol. 109, No. 14. (2005), pp. 6780-6. by Y. M. Rhee, V. S. Pande posted to diffusion molecular_simulation by sobolevnrm on 2007-05-25 14:23:18 as along with 1 group baker-group
	Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 32. (2006), pp. 11916-21. by P. M. Kasson, N. W. Kelley, N. Singhal, M. Vrljic, A. T. Brunger, V. S. Pande posted to biomembranes multiscale by sobolevnrm on 2007-05-25 14:23:17 as along with 1 group baker-group
	Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory [My Copy] Science, Vol. 313, No. 5784. (2006), pp. 200-4. by I. T. Suydam, C. D. Snow, V. S. Pande, Boxer posted to electrostatics by sobolevnrm on 2007-05-25 14:23:17 as along with 1 group baker-group
	Using massively parallel simulation and Markovian models to study protein folding: Examining the dynamics of the villin headpiece [My Copy] Journal of Chemical Physics, Vol. 124 (2006) by G. Jayachandran, V. Vishal, V. S. Pande posted to protein_folding by sobolevnrm on 2007-05-25 14:22:45 as along with 1 group baker-group
	Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins [My Copy] Journal of Chemical Physics, Vol. 119, No. 11. (2003), pp. 5740-61. by M. R. Shirts, J. W. Pitera, W. C. Swope, V. S. Pande posted to molecular_dynamics solvation by sobolevnrm on 2007-05-25 14:19:55 as along with 1 group baker-group
	Can Conformational Change Be Described by Only a Few Normal Modes? [My Copy] Biophysical Journal, Vol. 90, No. 5. (2006), pp. 1583-93. by P. Petrone, V. S. Pande posted to quasiharmonic_models by sobolevnrm on 2007-05-25 14:19:53 as along with 1 group baker-group
	Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water [My Copy] Journal of Chemical Physics, Vol. 123 (2005) by S. P. Elmer, S. Park, V. S. Pande posted to diffusion protein_folding statistical_mechanics by sobolevnrm on 2007-05-25 14:18:43 as along with 1 group baker-group
	Foldamer dynamics expressed via Markov state models. II. State space decomposition [My Copy] Journal of Chemical Physics, Vol. 123 (2005) by S. P. Elmer, S. Park, V. S. Pande posted to protein_folding statistical_mechanics by sobolevnrm on 2007-05-25 14:18:43 as along with 1 group baker-group
	Direct calculation of the binding free energies of FKBP ligands [My Copy] Journal of Chemical Physics, Vol. 123 (2005) by H. Fujitani, Y. Tanida, M. Ito, et al.G. Jayachandran, C. D. Snow, M. D. Shirts, E. J. Sorin, V. S. Pande posted to protein-ligand_interactions by sobolevnrm on 2007-05-25 14:18:25 as along with 1 group baker-group
	Does Water Play a Structural Role in the Folding of Small Nucleic Acids? [My Copy] Biophysical Journal, Vol. 88, No. 4. (2005), pp. 2516-24. by E. J. Sorin, Y. M. Rhee, V. S. Pande posted to nucleic_acids by sobolevnrm on 2007-05-25 14:16:05 as along with 1 group baker-group
	How Well Can Simulation Predict Protein Folding Kinetics and Thermodynamics? [My Copy] Annual Review of Biophysics and Biomolecular Structure (2005) by C. D. Snow, E. J. Sorin, Y. M. Rhee, V. S. Pande posted to protein_folding by sobolevnrm on 2007-05-25 14:15:42 as along with 1 group baker-group
	Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations [My Copy] Biophysical Journal, Vol. 85, No. 2. (2003), pp. 790-803. by E. J. Sorin, Y. M. Rhee, B. J. Nakatani, V. S. Pande posted to electrostatics molecular_dynamics nucleic_acids solvation by sobolevnrm on 2007-05-25 14:14:06 as along with 1 group baker-group
	Molecular Dynamics Simulation of Lipid Reorientation at Bilayer Edges [My Copy] Biophysical Journal, Vol. 86, No. 6. (2004), pp. 3744-9. by P. M. Kasson, V. S. Pande posted to biomembranes by sobolevnrm on 2007-05-25 14:10:27 as along with 1 group baker-group
	Absolute comparison of simulated and experimental protein-folding dynamics [My Copy] Nature, Vol. 420, No. 6911. (2002), pp. 102-106. by C. D. Snow, H. Nguyen, V. S. Pande, M. Gruebele posted to protein_folding by sobolevnrm on 2007-05-25 14:08:29 as along with 1 group baker-group
	Simulations of the role of water in the protein-folding mechanism [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 17. (2004), pp. 6456-6461. by Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, V. S. Pande posted to protein_folding solvation by sobolevnrm on 2007-05-25 14:07:52 as along with 1 group baker-group
	Simulations of the role of water in the protein-folding mechanism [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 17. (2004), pp. 6456-6461. by Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, V. S. Pande posted to protein_folding solvation by sobolevnrm on 2007-05-25 14:07:52 as along with 1 group baker-group

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electrostatics	2020
solvation	1604
biomembranes	1512
statistical_mechanics	674
mathematics	623
bioinformatics	611
diffusion	528
molecular_dynamics	514
molecular_simulation	511
nucleic_acids	479
multiscale	409
quasiharmonic_models	338
structure	327
nanotech	286
allostery	269
beyond_mean_field	210
review	209
protein_folding	203
protein-protein_interactions	187
systems_biology	186
software	178
kinetics	170
acetylcholinesterase	167
protein-ligand_interactions	167
misc	151
biological_systems	150
experimental_methodology	147
thrombin	143
correlated_mutations	126
neuromuscular_junctions	121
pka	119
protein-nucleic_acid_interactions	116
sterols	113
drug_design	111
outer_hair_cells	104
metalloregulation	96
database	96
cellular_mechanics	91
structure_prediction	91
imaging	86
ontology	85
ccne	84
protein-membrane_interactions	83
quantum_mechanics	83
nonpolar	80
nerve_agents	78
nitric_oxide	74
career	71
visualization	69
emulsions	67
interfaces	57
ligand-membrane_interactions	57
nmr	52
cancer	51
protein_engineering	48
free_energy	44
mechanics	44
integral_equation	41
clustering	41
teaching	39
ion_channels	38
enhanced_sampling	36
ultrasound	33
perfluorocarbons	31
statistics	27
sccne	24
graph_theory	24
programming	23
helicase	22
informatics	21
pgdh	21
flexoelectric	20
fluid_mechanics	17
ribosome	17
drug_delivery	15
molecular-simulation	15
quasiharmonic-models	15
geometry	14
gating	13
nanotechnology	13
toxicity	13
statistical-mechanics	12
apbs	11
funding	10
energy_landscapes	10
pdb2pqr	9
molecular-dynamics	8
nikr	8
cytoskeleton	7
cholesterol	6
electrochemistry	6
protein-protein-interactions	5
protein-ligand-interactions	5
finite_element	5
docking	4
single_molecule	4
protein-folding	4
nitric-oxide	4
nucleic-acids	3
hydrodynamics	3
finite_differences	3
ligand-membrane-interactions	3
scattering	3
thermodynamics	3
optimization	3
integral-equation	3
biodistribution	2
oxysterols	2
generalized_born	2
boundary_element	2
salicylate	2
conformation	2
neuroscience	2
ethics	2
systems-biology	2
nanoparticles	2
computational_geometry	2
quantum-mechanics	2
magnetism	2
protein-membrane-interactions	2
virus	2
protein-engineering	1
text_mining	1
data_mining	1
lipids	1
mice	1
integral_equations	1
web	1
phosphatidylcholines	1
melittin	1
fluorescence_quenching	1
redox_potentials	1
protein-allostery	1
red_blood_cell	1
systems	1
hydrogen_bonds	1
protein-nucleic-acid-interactions	1
protein-design	1
colloid-complex	1
mutual-information	1
text-mining	1

sobolevnrm's Pande:VS [42 articles] Export

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