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Tag free_energy [145 articles]

Recent papers classified by the tag free_energy.
  • Optimal Estimates of Free Energies from Multistate Nonequilibrium Work Data
    Physical Review Letters, Vol. 96, No. 10. (2006)
    by Paul Maragakis, Martin Spichty, Martin Karplus
    posted to free_energy nonequilibrium by sotaro on 2006-03-23 09:14:15 as *** along with 2 people madhadron maragakis
  • Multicanonical simulations step by step
    Computer Physics Communications, Vol. 153, No. 3. (1 July 2003), pp. 397-406.
    by Bernard A Berg
    posted to enrtopy free_energy multicanonical_ensemble by rabio on 2007-02-13 12:54:49 as **
  • Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy.
    Biophys J, Vol. 86, No. 1 Pt 1. (January 2004), pp. 67-74.
    by JM Swanson, RH Henchman, JA McCammon
    posted to drug_design free_energy by onufriev on 2007-10-29 20:19:02 as read along with 2 people lillekatt mleis
  • Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin.
    J Mol Biol, Vol. 237, No. 5. (15 April 1994), pp. 602-614.
    by AS Yang, B Honig
    posted to free_energy pk protein_electrostatics by onufriev on 2007-11-12 16:16:23 as read along with 1 person and 1 group cat_worth structural_bioinformatics
  • Estimating Ratios of Normalizing Constants Using Linked Importance Sampling
    (8 Nov 2005)
    by Radford M Neal
    posted to free_energy monte_carlo by markdewing on 2005-11-22 02:24:57 as **** along with 1 person DavidBickel
  • Molecular dynamics simulations of martensitic transitions
    Philosophical Magazine, Part B, Vol. 80 (February 2000), pp. 183-194.
    by P Entel, R Meyer, K Kadau
    posted to eam free_energy iron martensitic molecular_dynamics phase_transition by luisand on 2007-12-18 09:19:44 as **
  • Characterization of Fe potentials with respect to the stability of the bcc and fcc phase
    Modelling and Simulation in Materials Science and Engineering, Vol. 16, No. 3. (2008), 035005.
    by Cemal Engin, Luis Sandoval, Herbert M Urbassek
    posted to eam free_energy iron personal solids by luisand on 2008-04-09 17:19:14 as read
  • Numerical evaluation of the exact phase diagram of an empirical Hamiltonian: Embedded atom model for the Au-Ni system
    Physical Review B, Vol. 66, No. 5. (2002), 054201.
    by Ogando, M Caro, A Caro
    posted to alloys eam free_energy melting molecular_dynamics phase_diagram phase_transition by luisand on 2007-12-20 10:14:15 as **
  • Why Is It So Difficult To Simulate Entropies, Free Energies, and Their Differences?
    Acc. Chem. Res., Vol. 34, No. 7. (17 July 2001), pp. 607-614.
    by WP Reinhardt, MA Miller, LM Amon
    posted to free_energy molecular_dynamics phase_transition by luisand on 2007-12-19 21:55:38 as **
  • Free-energy calculations and the melting point of Al
    Physical Review B, Vol. 46, No. 1. (1 July 1992), 21.
    by J Mei, JW Davenport
    posted to eam free_energy molecular_dynamics by luisand on 2007-12-20 10:02:10 as **
  • Phase diagram of an empirical potential: The case of Fe-Cu
    Phys. Rev. B, Vol. 68, No. 21. (December 2003), 214205.
    by EM Lopasso, M Caro, A Caro, PE Turchi
    posted to eam free_energy iron molecular_dynamics phase_transition by luisand on 2007-12-17 11:46:34 as **
  • Martensitic transformations: first-principles calculations combined with molecular-dynamics simulations
    The European Physical Journal B - Condensed Matter and Complex Systems, Vol. 5, No. 3. (6 October 1998), pp. 379-388.
    by P Entel, R Meyer, K Kadau, HC Herper, E Hoffmann
    posted to eam free_energy iron martensitic molecular_dynamics phase_transition by luisand on 2007-12-17 11:44:05 as read
  • Martensite-austenite transition and phonon dispersion curves of Fe_1-xNi_x studied by molecular-dynamics simulations
    Physical Review B, Vol. 57, No. 9. (1 March 1998), 5140.
    by R Meyer, P Entel
    posted to eam free_energy iron martensitic molecular_dynamics phase_transition phonon_dispersion by luisand on 2007-12-17 11:38:46 as read
  • Efficient free energy calculations by variationally optimized metric scaling: Concepts and applications to the volume dependence of cluster free energies and to solid--solid phase transitions
    The Journal of Chemical Physics, Vol. 113, No. 17. (2000), pp. 7035-7046.
    by Mark A Miller, William P Reinhardt
    posted to free_energy molecular_dynamics by luisand on 2007-11-28 11:18:27 as **
  • Physics of New Materials (Springer Series in Materials Science)
    (30 October 1998)
    by Francisco E Fujita
    posted to bain_transformation free_energy iron martensitic metals new_materials nishiyama_transformation phase_transition thermodynamics by luisand on 2007-12-21 10:42:58 as **
  • Atomistic Investigations of the Thermodynamical Stability and Martensitic Nucleation of Fe 80 Ni 20 Nanoparticles
    Phase Transitions, Vol. 75, No. 1. (2002), pp. 59-65.
    by K Kadau, P Entel
    posted to alloys bain_transformation eam free_energy iron many_body martensitic molecular_dynamics by luisand on 2007-12-21 10:37:50 as **
  • Fcc-bcc transition for Yukawa interactions determined by applied strain deformation
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 69, No. 5. (2004)
    by Robert S Hoy, Mark O Robbins
    posted to bain_transformation free_energy molecular_dynamics yukawa by luisand on 2007-12-21 10:33:25 as **
  • Calculation of ligand binding free energies from molecular dynamics simulations
    International Journal of Quantum Chemistry, Vol. 69, No. 1. (1998), pp. 77-88.
    by J Marelius, T Hansson, J Åqvist
    posted to free_energy md by LamBras on 2007-11-23 12:41:12 as ** along with 1 person kazemi
  • Pathway and Endpoint Free Energy Calculations for Cyclic Nucleotide Binding to HCN Channels
    Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. L90-92.
    by Lei Zhou, Steven A Siegelbaum
    posted to protein-ligand md_simulation free_energy electrostatics binding by jmccammon on 2008-07-03 00:57:58 as read
  • From the Cover: A dry ligand-binding cavity in a solvated protein
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6296-6301.
    by Johan Qvist, Monika Davidovic, Donald Hamelberg, Bertil Halle
    posted to solvation protein-ligand md_simulation free_energy by jmccammon on 2008-05-26 21:33:02 as read
  • Calculation of protein-ligand binding free energy by using a polarizable potential
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295.
    by Dian Jiao, Pavel A Golubkov, Thomas A Darden, Pengyu Ren
    posted to protein-ligand md_simulation free_energy binding by jmccammon on 2008-05-26 21:31:42 as read along with 2 people and 1 group sobolevnrm biehl baker-group
  • Failure of the work-Hamiltonian connection for free-energy calculations.
    Phys Rev Lett, Vol. 100, No. 2. (18 January 2008)
    by JM Vilar, JM Rubi
    posted to free_energy hamiltonian physics statistical_mechanics thermodynamics by jjray on 2008-03-14 17:31:10 as **
  • Calculation of the Entropy and Free Energy from Monte Carlo Simulations of a Peptide Stretched by an External Force
    J. Phys. Chem. B, Vol. 109, No. 46. (24 November 2005), pp. 21963-21970.
    by S Cheluvaraja, H Meirovitch
    posted to data entropy free_energy molecular_dynamics protein_structure by hmk on 2008-04-03 19:54:33 as **
  • Computational design of antibody-affinity improvement beyond in vivo maturation.
    Nat Biotechnol (23 September 2007)
    by Shaun M M Lippow, K Dane D Wittrup, Bruce Tidor
    posted to data free_energy graphical_models protein_design protein_fold protein_structure by hmk on 2007-10-31 14:06:33 as ***** along with 1 person zwang
  • Flexibility and packing in proteins
    PNAS, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279.
    by Bertil Halle
    posted to free_energy protein_structure by hmk on 2007-02-23 23:57:08 as ** along with 3 people and 2 groups ana aqeel allmensch structural_bioinformatics Bioinformatics
  • Construction of effective free energy landscape from single-molecule time series
    Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302.
    by Akinori Baba, Tamiki Komatsuzaki
    posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:49:47 as ** along with 6 people and 1 group hsekiguc zwang cactus sobolevnrm Diego_Prada arnaudriegert baker-group
  • Protein Free Energy Landscapes Remodeled by Ligand Binding
    Biophys. J., Vol. 93, No. 2. (15 July 2007), pp. 579-585.
    by Troy C Messina, David S Talaga
    posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:46:10 as **
  • The atomic structure of protein-protein recognition sites
    Journal of Molecular Biology, Vol. 285, No. 5. (5 February 1999), pp. 2177-2198.
    by Loredana L Conte, Cyrus Chothia, Joel Janin
    posted to data free_energy graphical_models protein_protein_interactions by hmk on 2008-03-15 22:31:01 as **
  • A simple physical model for binding energy hot spots in protein-protein complexes.
    Proc Natl Acad Sci U S A, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121.
    by T Kortemme, D Baker
    posted to protein_protein_interactions molecular_mechanics free_energy data alternatives by hmk on 2008-06-01 00:24:36 as ** along with 5 people and 1 group skoddet lna jwm bicko cjeans Nielsen group
  • "Mining Minima": Direct Computation of Conformational Free Energy
    J. Phys. Chem. A, Vol. 101, No. 8. (20 February 1997), pp. 1609-1618.
    by MS Head, JA Given, MK Gilson
    posted to free_energy by hmk on 2008-04-03 20:52:59 as **
  • Calculation of protein-ligand binding affinities.
    Annu Rev Biophys Biomol Struct, Vol. 36 (2007), pp. 21-42.
    by MK Gilson, HX Zhou
    posted to alternatives binding data free_energy by hmk on 2008-04-03 20:50:50 as ** along with 4 people ras dimka neils ashaytan
  • Extraction of configurational entropy from molecular simulations via an expansion approximation
    The Journal of Chemical Physics, Vol. 127, No. 2. (2007)
    by Benjamin J Killian, Joslyn Y Kravitz, Michael K Gilson
    posted to free_energy protein_structure by hmk on 2008-04-03 20:46:55 as **
  • Large-scale characteristics of the energy landscape in protein-protein interactions.
    Proteins (11 October 2007)
    by Nicholas O'toole, Ilya A A Vakser
    posted to free_energy protein_folding protein_protein_interactions protein_structure by hmk on 2007-12-06 07:18:22 as ** along with 2 people bicko paulschlesinger
  • Thermodynamics of the interaction of barnase and barstar: changes in free energy versus changes in enthalpy on mutation
    Journal of Molecular Biology, Vol. 267, No. 3. (4 April 1997), pp. 696-706.
    by Christian Frisch, Gideon Schreiber, Christopher M Johnson, Alan R Fersht
    posted to docking free_energy protein_structure by hmk on 2007-02-23 16:26:49 as **
  • A new class of models for computing receptor-ligand binding affinities
    Chemistry & Biology, Vol. 4, No. 2. (1997), pp. 87-92.
    by Michael K Gilson, James A Given, Martha S Head
    posted to free_energy molecular_dynamics protein_protein_interactions by hmk on 2008-04-03 20:40:59 as **
  • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.
    J Mol Biol, Vol. 320, No. 2. (5 July 2002), pp. 369-387.
    by R Guerois, JE Nielsen, L Serrano
    posted to protein_structure free_energy by hmk on 2007-02-23 14:53:30 as ** along with 4 people apaydin aalibes chad_davis carlescorbi
  • Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
    PNAS, Vol. 103, No. 26. (27 June 2006), pp. 9885-9890.
    by Payel Das, Mark Moll, Hernan Stamati, Lydia E Kavraki, Cecilia Clementi
    posted to dynamics free_energy graphical_models protein_folding by hmk on 2007-12-06 00:10:32 as ** along with 2 people and 2 groups samjlord sobolevnrm moernerlab baker-group
  • Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
    Journal of Computational Chemistry, Vol. 28, No. 12. (2007), pp. 2059-2066.
    by Liliana Wroblewska, Jeffrey Skolnick
    posted to alternatives data decoy decoy_detection free_energy molecular_dynamics by hmk on 2007-12-12 16:49:46 as ** along with 1 person pawelp
  • Sampling Realistic Protein Conformations Using Local Structural Bias.
    PLoS Comput Biol, Vol. 2, No. 9. (22 September 2006)
    by Thomas Hamelryck, John T T Kent, Anders Krogh
    posted to free_energy graphical_models protein_fold protein_structure statistics by hmk on 2007-10-31 17:54:26 as ***** along with 2 people wouterboomsma j3xucite
  • Recognition of errors in three-dimensional structures of proteins.
    Proteins, Vol. 17, No. 4. (December 1993), pp. 355-362.
    by MJ Sippl
    posted to decoy_detection free_energy graphical_models by hmk on 2007-04-28 23:50:26 as ** along with 1 person chad_davis
  • Unified approach for molecular dynamics and density-functional theory
    Physical Review Letters, Vol. 55 (November 1985), pp. 2471-2474.
    by R Car, M Parrinello
    posted to free_energy molecular_dynamics physics quantum_physics by hmk on 2008-04-10 07:07:29 as ** along with 2 people and_ped10 eyliu
  • The statistical-thermodynamic basis for computation of binding affinities: a critical review.
    Biophys J, Vol. 72, No. 3. (March 1997), pp. 1047-1069.
    by MK Gilson, JA Given, BL Bush, JA McCammon
    posted to entropy free_energy molecular_dynamics physics protein_structure review by hmk on 2008-04-03 20:07:07 as ** along with 1 person and 1 group ssomani structure-bii
  • Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 164-179.
    by Amarda Shehu, Cecilia Clementi, Lydia E Kavraki
    posted to free_energy loops protein_structure by hmk on 2007-03-23 01:39:24 as ** along with 6 people and 2 groups apaydin nigham aqeel yongzhao elham sobolevnrm TSRI_MGL baker-group
  • The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees
    BMC Bioinformatics, Vol. 7, No. Suppl 1. (2006)
    by Cornelis Albers, Martijn Leisink, Hilbert Kappen
    posted to free_energy graphical_models by hmk on 2007-03-07 02:40:46 as **
  • Structural stability of oligomeric proteins: A mean-field theoretical approach
    Journal of Computer-Aided Materials Design, Vol. V4, No. 1. (1 April 1997), pp. 1-8.
    by Armin R Vã¶lkel, Jaan Noolandi
    posted to free_energy inference protein_structure by hmk on 2007-03-09 00:04:55 as **
  • Streptavidin Tetramerization and 2D Crystallization: A Mean-Field Approach
    Biophys. J., Vol. 80, No. 4. (1 April 2001), pp. 2004-2010.
    by T Coussaert, AR Volkel, J Noolandi, AP Gast
    posted to free_energy graphical_models inference protein_structure by hmk on 2007-03-09 00:01:52 as **
  • Decomposition of the Free Energy of a System in Terms of Specific Interactions : Implications for Theoretical and Experimental Studies
    Journal of Molecular Biology, Vol. 240, No. 2. (7 July 1994), pp. 167-176.
    by Alan E Mark, Wilfred F van Gunsteren
    posted to docking free_energy protein_structure by hmk on 2007-02-23 16:39:50 as **
  • Convergent Tree-Reweighted Message Passing for Energy Minimization
    IEEE Trans. Pattern Anal. Mach. Intell., Vol. 28, No. 10. (October 2006), pp. 1568-1583.
    by Vladimir Kolmogorov
    posted to free_energy graphical_models inference by hcs on 2007-03-10 21:21:31 as ** along with 1 person iris_2001
  • Estimation and Marginalization Using the Kikuchi Approximation Methods
    Neural Computation, Vol. 17, No. 8. (August 2005), pp. 1836-1873.
    by Payam Pakzad, Venkat Anantharam
    posted to inference machine_learning free_energy graphical_models by hcs on 2007-03-10 21:04:41 as **
  • Semi-Supervised Learning -- A Statistical Physics Approach
    (5 Apr 2006)
    by Gad Getz, Noam Shental, Eytan Domany
    posted to free_energy graphical_models machine_learning semi_supervised_learning spectral_graph_theory by hcs on 2007-04-08 18:50:26 as ** along with 1 person proportional
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