Tag free_energy [at least 200 articles] Export

Recent papers classified by the tag free_energy.

	Replacement Factor in a Linear Chain [My Copy] Physical Review Online Archive (Prola), Vol. 182, No. 1. (Jun 1969), pp. 339-342. by J. Lothe, G. M. Pound posted to theory physics partition_function linear_chain free_energy by chiufanlee on 2009-11-23 14:00:06 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
	Topological defects in the Abrikosov lattice of vortices in type-II superconductors [My Copy] Physical Review B, Vol. 51, No. 17. (May 1995), pp. 11887-11902. by M. J. W. Dodgson, M. A. Moore posted to topological_defects superconductivity lowest_landau_level free_energy defect_solutions abrikosov_lattice by tictacgo on 2009-11-14 12:06:16 as
	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 protein_dynamics protein-ligand molecular_dynamics_simulations md_simulation free_energy entropy drug-discovery binding by jmccammon to the group McCammon on 2009-11-12 01:00:02 as along with 7 people and 1 group cchang agrossfield anuragsethi sobolevnrm dr_proton qshao paulschlesinger Chang group
	Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2583-2588. by Wei Jiang, Milan Hodoscek, Benoît Roux posted to simulation free_energy by qshao on 2009-11-11 00:02:05 as along with 1 person sobolevnrm
	Predictive coding under the free-energy principle [My Copy] Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 364, No. 1521. (12 May 2009), pp. 1211-1221. by Karl Friston, Stefan Kiebel posted to theoretical_neuroscience predictive_coding perceptual_inference hierarchical_models free_energy dynamical_systems bayesian bayes by flieder on 2009-11-10 17:31:07 as along with 1 person PaperCollector
	Replica method and finite volume corrections [My Copy] (6 Nov 2009) by Matteo Campellone, Giorgio Parisi, Miguel A. Virasoro posted to replica_method mean_field free_energy finite_volume by marinari on 2009-11-09 09:27:13 as
	The Ising spin glass in finite dimensions: a perturbative study of the free energy [My Copy] (2 Nov 2009) by Tamas Temesvari posted to spin_glass replica_method replica_field_theory perturbation_theory ising free_energy finite_d by marinari on 2009-11-04 11:06:47 as
	Unorthodox uses of Bennett's acceptance ratio method [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Gerhard König, Stefan Bruckner, Stefan Boresch posted to free_energy by ssomani on 2009-11-03 21:14:49 as along with 2 people agrossfield RamuAnandakrishnan
	Distinguishing between smooth and rough free energy barriers in protein folding [My Copy] Biochemistry, Vol. 0, No. ja. (0000) by Stefano Gianni, Maurizio Brunori, Per Jemth, Mikael Oliveberg, Mingjie Zhang posted to transition_states transition_state protein_stability pathways globular_proteins free_energy energy_barriers chevron by samcho on 2009-11-02 19:49:30 as
	Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2589-2594. by Luca Maragliano, Eric Vanden-Eijnden, Benoît Roux posted to molecular_simulation free_energy by sobolevnrm on 2009-10-31 00:16:11 as along with 1 person anuragsethi
	Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site [My Copy] Journal of Molecular Biology (24 September 2009) by Sarah E. Boyce, David L. Mobley, Gabriel Rocklin, Alan P. Graves, Ken A. Dill, Brian K. Shoichet posted to free_energy binding_affinity by ahmetbakan on 2009-10-19 01:46:38 as
	Activated Hopping, Barrier Fluctuations, and Heterogeneity in Glassy Suspensions and Liquids† [My Copy] The Journal of Physical Chemistry B, Vol. 108, No. 51. (1 December 2004), pp. 19729-19741. by K. S. Schweizer, E. J. Saltzman posted to three_circ_confinement thermodynamics liquid hard_sphere glass_transition free_energy entropy by ghunter on 2009-10-15 19:44:23 as along with 3 people elorenz weeks dchen
	Entropic barriers, activated hopping, and the glass transition in colloidal suspensions [My Copy] The Journal of Chemical Physics, Vol. 119, No. 2. (2003), pp. 1181-1196. by Kenneth S. Schweizer, Erica J. Saltzman posted to three_circ_confinement phase_transition hard_sphere glass_transition free_energy entropy colloidal_suspensions by ghunter on 2009-10-15 19:43:37 as along with 2 people dchen weeks
	Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 6. (1 June 2008), pp. 869-876. by William L. Jorgensen, Laura L. Thomas posted to free_energy by qshao on 2009-10-12 22:51:08 as along with 1 person rpetrenko
	pKa Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 37. (1 September 2005), pp. 17715-17733. by Demian Riccardi, Patricia Schaefer, Qiang Cui posted to pka free_energy by qshao on 2009-10-12 22:48:55 as along with 1 person flbarroso
	Prediction of the Water Content in Protein Binding Sites [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13337-13346. by Julien Michel, Julian Tirado-Rives, William L. Jorgensen posted to water_molecules solvation simulation_methodology protein-ligand monte_carlo md_simulation free_energy drug-discovery binding by jmccammon to the group McCammon on 2009-10-10 21:07:02 as along with 2 people snichols15 qshao
	Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics [My Copy] Journal of Computational Physics, Vol. 225, No. 1. (01 July 2007), pp. 509-527. by A. Donev, F. Stillinger, S. Torquato posted to three_circ_confinement thermodynamics simulation molecular_dynamics hard_sphere free_energy 3d 2d by ghunter on 2009-10-08 21:24:23 as
	Measuring Thermodynamic Length [My Copy] Physical Review Letters, Vol. 99, No. 10. (2007), 100602. by Gavin E. Crooks posted to transformation thermodynamic_system shannon jensen free_energy fisher equilibrium_statistical_mechanics acceptance_ratio by tictacgo on 2009-09-30 06:21:33 as along with 1 person and 1 group sobolevnrm baker-group
	Riemannian geometry in thermodynamic fluctuation theory [My Copy] Reviews of Modern Physics, Vol. 67, No. 3. (Jul 1995), pp. 605-659. by George Ruppeiner posted to thermodynamics tensor subsystems statistical_mechanics riemannian metric information_theory geometry free_energy fluctuations entropy curvature critical_point critical_exponents by tictacgo on 2009-09-30 06:19:47 as
	The energy–density landscape for soft spheres [My Copy] Journal of Physics: Condensed Matter, Vol. 15, No. 11. (2003), pp. S1243-S1251. by Robin J. Speedy posted to three_circ_confinement hard_sphere glass_transition free_energy by ghunter on 2009-09-25 00:32:54 as
	Free energy landscape approach to glass transition [My Copy] Journal of Non-Crystalline Solids, Vol. 352, No. 42-49. (15 November 2006), pp. 4843-4846. by T. Odagaki, T. Yoshidome, A. Koyama, A. Yoshimori posted to three_circ_confinement simulation glass_transition free_energy by ghunter on 2009-09-25 00:31:34 as
	Free energy landscape and cooperatively rearranging region in a hard sphere glass [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 2. (2007), 021506. by Takashi Yoshidome, Akira Yoshimori, Takashi Odagaki posted to simulation hard_sphere glass_transition free_energy 3d by ghunter on 2009-09-25 00:30:25 as
	Strengths and Weaknesses of Parallel Tempering [My Copy] (8 Aug 2009) by Jon Machta posted to parallel_tempering golf_course free_energy double_well by marinari on 2009-09-23 14:05:41 as along with 1 person dpf
	Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation [My Copy] Journal of Computational Chemistry, Vol. 30, No. 11. (2009), pp. 1664-1679. by Clara D. Christ, Wilfred F. Van Gunsteren posted to free_energy_difference free_energy by whitead to the group Jiang Research Group on 2009-09-16 22:20:02 as
	Covalent hydration energies for purine analogs by quantum chemical methods [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Selina C. Wang, Peter A. Beal, Dean J. Tantillo posted to free_energy covalent_hydration by whitead to the group Jiang Research Group on 2009-09-16 22:16:44 as
	Tracing the Entropy along a Reactive Pathway: The Energy As a Generalized Reaction Coordinate [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2193-2196. by Carine Michel, Alessandro Laio, Anne Milet posted to molecular_dynamics metadynamics free_energy entropy by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-09-15 12:05:20 as
	Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2165-2175. by Zhigang Zhou, Yanli Wang, Stephen H. Bryant posted to solvent_accessible_surface pb free_energy docking cathepsin by flbarroso on 2009-09-12 23:24:25 as
	Recovery of free energy branches in single molecule experiments [My Copy] (25 Jan 2009) by Ivan Junier, Alessandro Mossa, Maria Manosas, Felix Ritort posted to work_measurement tweezer single_molecule free_energy biophysics by marinari on 2009-09-10 11:41:51 as
	Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 1. (8 January 2009), pp. 267-274. by Yassmine Chebaro, Xiao Dong, Rozita Laghaei, Philippe Derreumaux, Normand Mousseau posted to proteins free_energy coarse-graining by edws on 2009-09-10 03:19:39 as
	How to obtain statistically converged MM/GBSA results [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Samuel Genheden, Ulf Ryde posted to free_energy by barry to the group McCammon on 2009-09-04 00:41:41 as along with 3 people pmung sobolevnrm RamuAnandakrishnan
	Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 38. (24 September 2009), pp. 12711-12720. by Jozef Hritz, Chris Oostenbrink posted to free_energy by qshao on 2009-09-02 22:52:52 as
	Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model [My Copy] Journal of Chemical Information and Modeling, Vol. 46, No. 6. (1 November 2006), pp. 2631-2637. by Ryan G. Coleman, Anna C. Salzberg, Alan C. Cheng posted to free_energy drug-design by flbarroso on 2009-08-16 20:33:27 as along with 3 people and 1 group caporaso cjeans tjimenez biomedical-nlp
	Predicting the energetics of osmolyte-induced protein folding/unfolding [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 42. (18 October 2005), pp. 15065-15068. by Matthew Auton, D. Wayne Bolen posted to free_energy osmolyte protein structure by qshao on 2009-07-31 23:46:41 as
	Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. [My Copy] Annual review of physical chemistry, Vol. 59, No. 1. (2008), pp. 573-601. by H. Hu, W. Yang posted to enzyme free_energy qmmm by flbarroso on 2009-07-25 22:27:34 as along with 1 person skoddet
	First Principle Theory for pKa Prediction at Molecular Level: pH Effects Based on Explicit Solvent Model [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10509-10514. by Kentaro Kido, Hirofumi Sato, Shigeyoshi Sakaki posted to electrostatics free_energy titration by jmccammon to the group McCammon on 2009-07-25 21:45:08 as along with 4 people and 1 group scampos qshao franklu310 whitead Jiang Research Group
	Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8967-8974. by Gerhard König, Stefan Boresch posted to born free_energy md solvation by flbarroso on 2009-07-21 19:19:22 as along with 2 people carlosjavierna sobolevnrm
	Dissecting the free energy of drug binding to DNA. [My Copy] Anti-cancer drug design, Vol. 11, No. 8. (December 1996), pp. 569-580. by J. B. Chaires posted to free_energy polyelectrolytes by flbarroso on 2009-07-21 19:05:06 as
	Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA. [My Copy] Journal of molecular biology, Vol. 274, No. 2. (28 November 1997), pp. 253-267. by M. Baginski, F. Fogolari, J. M. Briggs posted to antibiotics binding dna electrostatics free_energy by flbarroso on 2009-07-21 19:04:37 as
	Heat does not come in different colours: entropy–enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions [My Copy] Biophysical Chemistry, Vol. 93, No. 2-3. (28 November 2001), pp. 215-230. by A. Cooper posted to calorimetry entropy free_energy protein by flbarroso on 2009-07-21 18:26:49 as
	A method to calculate the probability distribution for systems with large energy barriers [My Copy] Chemical Physics, Vol. 213, No. 1-3. (15 December 1996), pp. 63-76. by O. Engkvist posted to free_energy simulation by flbarroso on 2009-07-21 15:30:45 as
	Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. [My Copy] Proteins, Vol. 39, No. 4. (1 June 2000), pp. 393-407. by Y. Y. Sham, Z. T. Chu, H. Tao, A. Warshel posted to free_energy hiv lie simulation by flbarroso on 2009-07-19 19:03:32 as
	On the electrostatic component of protein-protein binding free energy. [My Copy] PMC biophysics, Vol. 1, No. 1. (2008) by K. Talley, C. Ng, M. Shoppell, P. Kundrotas, E. Alexov posted to electrostatics free_energy protein-protein by flbarroso on 2009-07-19 19:01:55 as
	Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. [My Copy] Journal of computational chemistry, Vol. 25, No. 2. (30 January 2004), pp. 238-250. by H. Gohlke, D. A. Case posted to born free_energy pb protein-protein ras-raf solvent_accessible_surface by flbarroso on 2009-07-19 02:14:56 as along with 3 people bmduggan onufriev lillekatt
	Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation [My Copy] Biophysical Chemistry, Vol. 78, No. 1-2. (5 April 1999), pp. 113-126. by N. Prabhu posted to continnum dielectric discontinuities free_energy peptide simulation by flbarroso on 2009-07-19 02:00:57 as
	Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. [My Copy] The journal of physical chemistry. B, Vol. 111, No. 9. (8 March 2007), pp. 2242-2254. by D. L. Mobley, E. Dumont, J. D. Chodera, K. A. Dill posted to force-fields free_energy solvation by flbarroso on 2009-07-17 19:56:59 as along with 3 people tovrstra ashaytan bentenin
	Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. [My Copy] The Journal of chemical physics, Vol. 122, No. 13. (1 April 2005) by M. R. Shirts, V. S. Pande posted to free_energy md solvation water by flbarroso on 2009-07-17 19:52:50 as along with 1 person blackbart
	Exploring the Free Energy Landscape: From Dynamics to Networks and Back [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000415. by Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique, Fernando Falo posted to free_energy kinetics by sobolevnrm on 2009-07-17 12:53:57 as along with 6 people Fernando_FF kiekyon phoenixzxl edws zwang Diego_Prada
	Some Topics in the Theory of Fluids [My Copy] The Journal of Chemical Physics, Vol. 39, No. 11. (1963), pp. 2808-2812. by B. Widom posted to free_energy widom by flbarroso on 2009-07-17 02:01:48 as along with 2 people zhaidong mikaellund
	Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation [My Copy] Current Opinion in Structural Biology In Theory and simulation / Macromolecular assemblages, Vol. 17, No. 2. (April 2007), pp. 181-186. by H. Meirovitch posted to entropy folding free_energy protein simulation by flbarroso on 2009-07-17 00:08:38 as along with 4 people and 1 group sunhwan aqeel dmobley cchang Chang group

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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
physics	11
water	11
alternatives	10
docking	10
monte_carlo	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
absolute	2
alternative	2
backbone	2
chain	2
covalent_hydration	2
electrostatic_potentials	2
histogram	2
implicit	2
marrucci	2
math	2
networks	2
prediction	2
protein_fold	2
quantum_physics	2
specific_heat	2
sterols	2
structure	2
water_replacement	2

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