Group: baker-group - with tag free_energy [26 articles] Export

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

	Measuring Thermodynamic Length [My Copy] Physical Review Letters, Vol. 99, No. 10. (2007), 100602. by Gavin E. Crooks posted to free_energy statistical_mechanics by sobolevnrm to the group baker-group on 2009-05-15 12:46:43 as along with 1 person tictacgo
	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
	Inclusion mechanism of steroid drugs into beta-cyclodextrins. Insights from free energy calculations. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 22. (4 June 2009), pp. 7836-7843. by Wensheng Cai, Tingting Sun, Peng Liu, Christophe Chipot, Xueguang Shao posted to free_energy protein-ligand_interactions sterols by sobolevnrm to the group baker-group on 2009-05-11 12:28:12 as along with 1 person liuyz
	Lambda-dynamics free energy simulation methods. [My Copy] Journal of computational chemistry, Vol. 30, No. 11. (August 2009), pp. 1692-1700. by J. L. Knight, C. L. Brooks posted to free_energy molecular_dynamics review by sobolevnrm to the group baker-group on 2009-05-07 13:00:25 as along with 3 people ibuch klexa agrossfield
	Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Nidhi Singh, Arieh Warshel posted to free_energy solvation by sobolevnrm to the group baker-group on 2009-04-30 12:16:27 as
	Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Ren posted to electrostatics free_energy protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-04-28 12:22:54 as along with 2 people agrossfield flbarroso
	Large-Scale Application of High-Throughput Molecular Mechanics with Poisson-Boltzmann Surface Area for Routine Physics-Based Scoring of Protein-Ligand Complexes. [My Copy] Journal of medicinal chemistry (22 April 2009) by Scott P P. Brown, Steven W W. Muchmore posted to electrostatics free_energy protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-04-24 12:33:50 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
	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
	Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Sheeba J. Irudayam, Richard H. Henchman posted to free_energy protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-04-15 12:11:23 as along with 2 people agrossfield mijam
	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
	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
	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
	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
	In silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides [My Copy] Physical Review Letters, Vol. 102, No. 11. (2009), 118108. by Da W. Li, Rafael Brüschweiler posted to free_energy quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-26 11:37:09 as along with 2 people anna_yershova Diego_Prada
	Bounding the electrostatic free energies associated with linear continuum models of molecular solvation [My Copy] The Journal of Chemical Physics, Vol. 130, No. 10. (2009), 104108. by Jaydeep P. Bardhan, Matthew G. Knepley, Mihai Anitescu posted to electrostatic free_energy mathematics solvation by sobolevnrm to the group baker-group on 2009-03-26 11:36:03 as
	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
	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
	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
	Path integral analysis of Jarzynski's equality: Analytical results [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 2. (2009), 021122. by David D. L. Minh, Artur B. Adib posted to enhanced_sampling free_energy statistical_mechanics by sobolevnrm to the group baker-group on 2009-03-23 11:56:27 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
	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
	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 free_energy nmr by sobolevnrm to the group baker-group on 2009-03-04 13:10:43 as along with 2 people and 2 groups bmduggan barry structural_bioinformatics McCammon
	Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20227-20232. by Lianqing Zheng, Mengen Chen, Wei Yang posted to enhanced_sampling free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-03-04 13:07:09 as along with 3 people and 1 group sas iivanov phoenixzxl McCammon
	Tork: Conformational analysis method for molecules and complexes [My Copy] Journal of Computational Chemistry, Vol. 24, No. 16. (2003), pp. 1987-1998. by Chia-En Chang, Michael K. Gilson posted to free_energy molecular_simulation quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-04 13:05:08 as
	Computing conformational free energy by deactivated morphing [My Copy] The Journal of Chemical Physics, Vol. 129, No. 13. (2008), 134102. by Sanghyun Park, Albert Y. Lau, Benoît Roux posted to free_energy molecular_simulation by sobolevnrm to the group baker-group on 2008-12-28 15:32:37 as along with 3 people paddydu agrossfield sunhwan

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binding	75
md_simulation	62
protein-ligand	53
solvation	39
molecular_simulation	32
electrostatics	31
protein_structure	28
alchemical	27
drug-discovery	27
entropy	26
data	21
molecular_dynamics	21
md	17
protein-ligand_interactions	17
relative	17
graphical_models	15
review	15
protein_protein_interactions	14
simulation	12
water	11
alternatives	10
docking	10
monte_carlo	10
physics	10
methodology	9
pb	9
proteins	9
continnum	8
enhanced_sampling	8
hydration	8
thermodynamic_integration	8
conformation	7
ligand	7
statistical_mechanics	7
thermodynamics	7
drug_design	6
dynamics	6
folding	6
nmr	6
protein_dynamics	6
discussion_free_energy	5
glass_transition	5
hard_sphere	5
inference	5
nucleic_acids	5
potential_of_mean_force	5
protein	5
protein-protein	5
three_circ_confinement	5
umbrella_sampling	5
2009	4
accelerated_md	4
dna	4
flexibility	4
hiv	4
hydrophobicity	4
jarzynski	4
mmpbsa	4
pka	4
protein_folding	4
quasiharmonic_models	4
statistics	4
wham	4
adaptive_biasing_force	3
allosteric	3
coarse-graining	3
dielectric	3
expanded_ensemble	3
grand_canonical	3
ion_channel	3
lie	3
mean_field	3
metadynamics	3
methods	3
molecular_dynamics_simulations	3
nonequilibrium	3
protein_design	3
sampling	3
simulation_methodology	3
titration	3
umbrella	3
water_molecules	3
3d	2
alternative	2
backbone	2
covalent_hydration	2
electrostatic_potentials	2
free_energy_difference	2
hemaglutinin	2
implicit	2
landscape	2
marrucci	2
math	2
networks	2
pharma	2
protein_electrostatics	2
quantum_physics	2
specific_heat	2
sterols	2
water_replacement	2

Group: baker-group - with tag free_energy [26 articles] Export

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