Tag free-energy [at least 200 articles] Export

Recent papers classified by the tag free-energy.

	Archetypal energy landscapes [My Copy] Nature In Nature, Vol. 394, No. 6695. (20 August 1998), pp. 758-760. by David J. Wales, Mark A. Miller, Tiffany R. Walsh posted to pes_based free-energy energy_landscapes aux by Diego_Prada on 2009-12-03 16:55:53 as along with 2 people scampos aleperd
	Taking a Walk on a Landscape [My Copy] Science (New York, N.Y.) In Science, Vol. 293, No. 5530. (27 July 2001), pp. 612-613. by Charles L. Brooks, Jose N. Onuchic, David J. Wales posted to pes_based free-energy energy_landscape aux by Diego_Prada on 2009-12-03 16:32:50 as along with 1 person scampos
	Folding of the GB1 hairpin peptide from discrete path sampling [My Copy] The Journal of Chemical Physics, Vol. 121, No. 2. (2004), pp. 1080-1090. by David A. Evans, David J. Wales posted to pes_based free-energy aux by Diego_Prada on 2009-12-02 17:45:10 as
	Equilibrium density of states and thermodynamic properties of a model glass former [My Copy] The Journal of Chemical Physics, Vol. 127, No. 4. (2007), 044508. by Florent Calvo, Tetyana V. Bogdan, Vanessa K. de Souza, David J. Wales posted to pes_based free-energy energy_landscape aux by Diego_Prada on 2009-12-02 17:38:38 as
	Structure, Dynamics, and Thermodynamics of Clusters: Tales from Topographic Potential Surfaces [My Copy] Science, Vol. 271, No. 5251. (16 February 1996), pp. 925-929. by David J. Wales posted to pes_based free-energy aux by Diego_Prada on 2009-12-02 17:32:06 as
	Characterizing the network topology of the energy landscapes of atomic clusters [My Copy] The Journal of Chemical Physics, Vol. 122, No. 8. (2005), 084105. by Jonathan P. K. Doye, Claire P. Massen posted to pes_based free-energy cmn by Diego_Prada on 2009-12-02 17:13:48 as
	Exponential multiplicity of inherent structures [My Copy] Physical Review E, Vol. 59, No. 1. (Jan 1999), pp. 48-51. by Frank H. Stillinger posted to problems_fel_dof pes_based free-energy aux by Diego_Prada on 2009-12-02 17:10:17 as
	The energy landscapes and motions of proteins [My Copy] Science In Science, Vol. 254, No. 5038. (13 December 1991), pp. 1598-1603. by H. Frauenfelder, S. G. Sligar, P. G. Wolynes posted to free-energy energy_landscape by Diego_Prada on 2009-12-02 16:56:12 as along with 5 people paulymer xdeupi FilipeMaia naitsabes kjell
	Packing Structures and Transitions in Liquids and Solids [My Copy] Science, Vol. 225, No. 4666. (7 September 1984), pp. 983-989. by Frank H. Stillinger, Thomas A. Weber posted to pes_based glass_transition free-energy aux by Diego_Prada on 2009-12-02 16:39:33 as along with 2 people jenda_z chiufanlee
	Computation of Free Energy [My Copy] Helvetica Chimica Acta, Vol. 85, No. 10. (2002), pp. 3113-3129. by Wilfred F. van Gunsteren, Xavier Daura, Alan E. Mark posted to methods free-energy by Diego_Prada on 2009-12-02 12:23:33 as along with 1 person dmobley
	Calculation of free energy surfaces using the methods of thermodynamic perturbation theory [My Copy] Chemical Physics Letters, Vol. 142, No. 6. (25 December 1987), pp. 472-476. by Douglas J. Tobias, Charles L. Brooks posted to free-energy chapt_cmn by Diego_Prada on 2009-12-01 12:43:04 as
	A unified model of protein dynamics [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 13. (31 March 2009), pp. 5129-5134. by Hans Frauenfelder, Guo Chen, Joel Berendzen, et al.Paul W. Fenimore, HelÃ©n Jansson, Benjamin H. McMahon, Izabela R. Stroe, Jan Swenson, Robert D. Young posted to transition_states temperature_dependence t_dependence free-energy by Diego_Prada on 2009-12-01 12:20:46 as along with 8 people and 1 group paulymer Christophe abovell jdstevenson amishp sobolevnrm zwang kevinchannon baker-group
	Intermediates: ubiquitous species on folding energy landscapes? [My Copy] Current Opinion in Structural Biology, Vol. 17, No. 1. (February 2007), pp. 30-37. by David J. Brockwell, Sheena E. Radford posted to transition_states protein_folding free-energy by Diego_Prada on 2009-11-30 19:00:00 as
	Thermodynamics of protein folding: a microscopic view [My Copy] Biophysical Chemistry, Vol. 100, No. 1-3. (15 January 2003), pp. 367-395. by T. Lazaridis posted to protein_folding free-energy by Diego_Prada on 2009-11-30 17:07:45 as
	Enthalpic Contribution to Protein Stability: Insights from Atom-Based Calculations and Statistical Mechanics [My Copy] In Advances in Protein Chemistry Volume 47, Vol. 47 (1995), pp. 231-306. by T. Lazaridis, G. Archontis, M. Karplus posted to protein_folding free-energy by Diego_Prada on 2009-11-27 19:52:33 as along with 1 person flbarroso
	On the simulation of protein folding by short time scale molecular dynamics and distributed computing [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14122-14125. by Alan R. Fersht posted to short_time_simus free-energy by Diego_Prada on 2009-11-27 19:30:05 as along with 2 people doktornoe jheco
	Folding and binding cascades: Dynamic landscapes and population shifts [My Copy] Protein Science, Vol. 9, No. 1. (2000), pp. 10-19. by Sandeep Kumar, Buyong Ma, Chung-Jung Tsai, Neeti Sinha, Ruth Nussinov posted to free-energy by Diego_Prada on 2009-11-27 16:11:58 as
	Estimation of protein folding probability from equilibrium simulations [My Copy] The Journal of Chemical Physics, Vol. 122, No. 18. (2005), 184901. by Francesco Rao, Giovanni Settanni, Enrico Guarnera, Amedeo Caflisch posted to transition_states protein_folding free-energy cmn by Diego_Prada on 2009-11-26 18:21:55 as
	Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 4. (2008), pp. 1185-1195. by Stefanie Muff, Amedeo Caflisch posted to transition_states free-energy cmn chapt_cmn by Diego_Prada on 2009-11-26 17:24:35 as along with 1 person RamuAnandakrishnan
	FROM FOLDING THEORIES TO FOLDING PROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding [My Copy] Annual Review of Physical Chemistry, Vol. 52, No. 1. (2001), pp. 499-535. by Joan E. Shea, Charles L. Brooks posted to review protein_folding methods free-energy by Diego_Prada on 2009-11-25 16:26:15 as along with 3 people scampos fjc1 allmensch
	Conformational Dynamics and Ensembles in Protein Folding [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 36, No. 1. (2007), pp. 395-412. by Victor Muñoz posted to review protein_dynamics free-energy by Diego_Prada on 2009-11-25 15:48:01 as along with 1 person dfdong
	Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 1-23. by Halvor S. Hansen, Philippe H. Hünenberger posted to pmf free-energy by agrossfield on 2009-11-24 14:03:15 as
	Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 204-216. by Alexey K. Shaytan, Victor A. Ivanov, Konstantin V. Shaitan, Alexei R. Khokhlov posted to solvation pmf free-energy forcefield by agrossfield on 2009-11-24 13:57:39 as
	Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom [My Copy] Chemical Physics Letters, Vol. 194, No. 3. (26 June 1992), pp. 252-261. by S. Fischer, M. Karplus posted to transition_path reaction_paths problems_fel_dof methods free-energy by Diego_Prada on 2009-11-23 17:38:17 as along with 1 person ckmyo
	Free Energy for the Permeation of Na+ and Cl− Ions and Their Ion-Pair through a Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads [My Copy] Journal of the American Chemical Society, Vol. 131, No. 5. (11 February 2009), pp. 1706-1716. by Ilja V. Khavrutskii, Alemayehu A. Gorfe, Benzhuo Lu, J. Andrew McCammon posted to ions ion-membrane-interaction free-energy dmpc by softsimu on 2009-11-20 16:35:47 as along with 1 person and 1 group sobolevnrm baker-group
	Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 3. (1 May 2006), pp. 840-857. by Frank Noe, Dieter Krachtus, Jeremy C. Smith, Stefan Fischer posted to markov_state_models free-energy cmn aux by Diego_Prada on 2009-11-19 18:55:31 as along with 2 people aqeel toerst
	Identification of the protein folding transition state from molecular dynamics trajectories [My Copy] The Journal of Chemical Physics, Vol. 130, No. 12. (2009), 125104. by S. Muff, A. Caflisch posted to transition_states sampling markov_state_models free-energy by Diego_Prada on 2009-11-19 18:13:46 as
	Using generalized ensemble simulations and Markov state models to identify conformational states [My Copy] Methods, Vol. 49, No. 2. (3 October 2009), pp. 197-201. by Gregory R. Bowman, Xuhui Huang, Vijay S. Pande posted to markov_state_models free-energy by Diego_Prada on 2009-11-19 18:06:04 as along with 1 person apaydin
	Weighted ensemble dynamics simulations for detecting metastable states [My Copy] (2 Dec 2009) by Linchen Gong, Xin Zhou posted to free-energy dialanine cmn by Diego_Prada on 2009-11-19 11:53:58 as along with 1 person Fernando_FF
	Computing conformational free energy by deactivated morphing. [My Copy] The Journal of chemical physics, Vol. 129, No. 13. (7 October 2008) by Sanghyun Park, Albert Y. Lau, Benoît Roux posted to free-energy deltag by dimka on 2009-11-18 19:04:16 as
	Exploring energy landscapes of protein folding and aggregation. [My Copy] Frontiers in bioscience : a journal and virtual library, Vol. 13 (2008), pp. 4495-4516. by Normand Mousseau, Philippe Derreumaux posted to free-energy fre fibril_formation beta-hairpin aggregation by Diego_Prada on 2009-11-15 19:29:45 as
	Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 3. (2009), 031911. by Igor S. Tolokh, Victor Vivcharuk, Bruno Tomberli, C. G. Gray posted to free-energy antimicrobial-peptide by agrossfield on 2009-10-23 17:16:16 as
	Efficient exploration of energy landscapes [My Copy] (14 Oct 2009) by Martin Mann, Konstantin Klemm posted to transition_states mutual-information mc markov free-energy by Diego_Prada on 2009-10-20 19:21:50 as along with 2 people Fernando_FF apocapoc
	Generalized Langevin models of molecular dynamics simulations with applications to ion channels [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134102. by Dan Gordon, Vikram Krishnamurthy, Shin H. Chung posted to langevin ion-channel free-energy by agrossfield on 2009-10-07 20:57:15 as along with 1 person dlimmer
	Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134110. by David D. L. Minh, John D. Chodera posted to free-energy by agrossfield on 2009-10-07 20:55:44 as along with 1 person dlimmer
	Graph-based analysis of kinetics on multidimensional potential-energy surfaces [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 3. (2009), 036112. by T. Okushima, T. Niiyama, K. S. Ikeda, Y. Shimizu posted to transition_path qha kinetic_models free-energy first_passage cmn by Diego_Prada on 2009-10-05 17:07:19 as
	Rapid equilibrium sampling initiated from nonequilibrium data [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 47. (24 November 2009), pp. 19765-19769. by Xuhui Huang, Gregory R. Bowman, Sergio Bacallado, Vijay S. Pande posted to nonequilibrium markov_state_models markov free-energy by Diego_Prada on 2009-10-05 16:42:54 as along with 2 people doktornoe apaydin
	Flexibility and packing in proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279. by Bertil Halle posted to protein_flexibility protein_dynamics gnm free-energy by Diego_Prada on 2009-09-19 15:55:12 as along with 7 people and 3 groups edws barry sobolevnrm ana aqeel allmensch hmk baker-group structural_bioinformatics Bioinformatics
	Dynamic personalities of proteins [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972. by Katherine Henzler-Wildman, Dorothee Kern posted to proteins protein_folding protein_dynamics md free-energy by Diego_Prada on 2009-09-19 15:39:20 as along with 19 people and 1 group victorclaessen saravan xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
	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 free-energy collective_motions cmn allostery active_site by Diego_Prada on 2009-09-17 19:28:04 as along with 7 people and 2 groups anuragsethi bmduggan allmensch guhjy sobolevnrm barry jmccammon baker-group McCammon
	Structuring and sampling complex conformation space: Weighted ensemble dynamics simulations [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 2. (2009), 026707. by Linchen Gong, Xin Zhou posted to pca free-energy cmn by Diego_Prada on 2009-09-17 19:04:45 as
	A Topographic View of Supercooled Liquids and Glass Formation [My Copy] Science, Vol. 267, No. 5206. (31 March 1995), pp. 1935-1939. by Frank H. Stillinger posted to relaxation_processes glass_transition free-energy by Diego_Prada on 2009-09-17 18:52:02 as along with 5 people ruvido cgguido kedmond weeks dchen
	Network Structure of Protein Folding Pathways [My Copy] (7 May 2007) by Erzsebet Ravasz, S. Gnanakaran, Zoltan Toroczkai posted to short-peptides free-energy cmn by Diego_Prada on 2009-09-17 16:11:59 as
	Conformational entropy of alanine versus glycine in protein denatured states [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 8. (20 February 2007), pp. 2661-2666. by Kathryn A. Scott, Darwin O. V. Alonso, Satoshi Sato, Alan R. Fersht, Valerie Daggett posted to hexapeptide glycine free-energy conformational_entropy alanine by Diego_Prada on 2009-09-17 12:38:50 as
	New method to analyze simulations of activated processes [My Copy] The Journal of Chemical Physics, Vol. 126, No. 13. (2007), 134103. by Jan Wedekind, Reinhard Strey, David Reguera posted to stochastic_processes kinetic_models free-energy first_passage by Diego_Prada on 2009-09-15 17:23:41 as along with 1 person janw
	Kinetic Reconstruction of the Free-Energy Landscape [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 35. (4 September 2008), pp. 11060-11063. by Jan Wedekind, David Reguera posted to kinetic_models free-energy first_passage by Diego_Prada on 2009-09-15 17:21:40 as along with 3 people janwedekind paulschlesinger michaelbussmann
	Dissipation: The Phase-Space Perspective [My Copy] Physical Review Letters, Vol. 98, No. 8. (2007), 080602. by R. Kawai, J. M. R. Parrondo, C. Van den Broeck posted to work_theorem stochastic_processes out_of_equilibrium free-energy by Diego_Prada on 2009-09-15 16:47:43 as along with 2 people chiufanlee madhadron
	Massively parallel computation of absolute binding free energy with well-equilibrated states [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 2. (2009), 021914. by Hideaki Fujitani, Yoshiaki Tanida, Azuma Matsuura posted to new molecular-dynamics free-energy binding by dcheong on 2009-09-09 02:26:45 as
	Fragment-Based Computation of Binding Free Energies by Systematic Sampling. [My Copy] Journal of chemical information and modeling, Vol. 49, No. 8. (17 July 2009), pp. 1901-1913. by Matthew Clark, Siavash Meshkat, George T. Talbot, Paolo Carnevali, Jeffrey S. Wiseman posted to free-energy by carlosjavierna on 2009-09-05 03:34:15 as along with 1 person ubcg08l
	Minimum free-energy path of homogenous nucleation from the phase-field equation [My Copy] The Journal of Chemical Physics, Vol. 130, No. 24. (2009), 244507. by Masao Iwamatsu posted to theory physics phase-field-crystal nucleation free-energy by chiufanlee on 2009-09-04 13:28:32 as along with 1 person dlimmer

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cmn	22
hexapeptide	21
binding	20
abf	18
protein_folding	18
aux	17
perturbation	17
pmf	16
protein	15
folding	14
protein_dynamics	14
molecular_dynamics	13
chapt_cmn	12
md	12
simulation	11
dynamics	10
free-energy-adaptive	10
free-energy-pmf	10
ligand	10
markov	10
proteins	10
short-peptides	10
stochastic_processes	10
conformation	9
molecular	9
plos	9
molecular-dynamics	8
pes_based	8
solvation	8
transition_states	8
complex_systems	7
pca	7
potential	7
umbrella-sampling	7
dialanine	6
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residue-residue	6
theory	6
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articulo	5
beta-hairpin	5
hydrophobicity	5
jarzynski	5
mc	5
methods	5
modeling	5
networks	5
sampling	5
thermodynamics	5
wham	5
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coarse-graining	4
dna	4
electrostatics	4
hp_model	4
ion	4
markov_state_models	4
membrane	4
poisson-boltzmann	4
qha	4
reaction_paths	4
ab-initio	3
accelerated-molecular-dynamics	3
affinity	3
chemistry	3
cholesterol	3
communities	3
computer	3
dihedral	3
dpca	3
entropy	3
free-energy-landscape	3
hot	3
kinetic_models	3
ligand-binding	3
md_history	3
micelles	3
molecular-dynamics-simulations	3
monte-carlo	3
nonequilibrium	3
peptides	3
polymer	3
receptor	3
review	3
simulations	3
statistical_mechanics	3
technique	3
ti	3
allostery	2
deltag	2
landscape	2
lipid	2
motor	2
parametrization	2
problems_fel_dof	2
replica-exchange	2
statistical_potential	2

Tag free-energy [at least 200 articles] Export

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