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	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 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
	Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules [My Copy] posted to sampling free-energy by Diego_Prada on 2009-11-19 17:48:28 as along with 1 person barry
	Weighted ensemble dynamics simulation for detecting metastable states in complex conformational spaces [My Copy] (18 Nov 2009) by Linchen Gong, Xin Zhou posted to free-energy dialanine cmn by Diego_Prada on 2009-11-19 11:53:58 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
	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 1 person apocapoc
	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 (29 September 2009) 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
	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 18 people and 1 group 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 1 person madhadron
	Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 7. (10 July 2009), e1000428. by Lucy R. Allen, Sergei V. Krivov, Emanuele Paci posted to dihedral free-energy short-peptides by Diego_Prada on 2009-07-10 11:52:24 as along with 2 people zwang melo_mcr
	Theory for Protein Folding Cooperativity: Helix Bundles [My Copy] Journal of the American Chemical Society, Vol. 131, No. 6. (18 February 2009), pp. 2306-2312. by Kingshuk Ghosh, K. A. Dill posted to free-energy statistical_models by Diego_Prada on 2009-07-02 12:47:05 as along with 1 person carlosjavierna
	Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 8. (1 February 2008), pp. 2456-2465. by Mey Khalili, David J. Wales posted to first_passage free-energy protein_dynamics qha reaction_paths transition_path transition_states by Diego_Prada on 2009-07-02 12:02:29 as
	Refined kinetic transition networks for the GB1 hairpin peptide [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 18. (2009), pp. 3341-3354. by Joanne M. Carr, David J. Wales posted to beta-hairpin first_passage free-energy hexapeptide protein_dynamics protein_folding qha reaction_paths short-peptides transition_path transition_states by Diego_Prada on 2009-07-02 11:55:15 as
	Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks [My Copy] (24 Jun 2009) by Gregg Lois, J. Blawzdziewicz, Corey S. O'Hern posted to cmn coarse-grained complex_systems first_passage free-energy hp_model networks protein_dynamics protein_folding proteins reaction_paths transition_path by Diego_Prada on 2009-06-25 16:27:33 as
	A Probabilistic Model of RNA Conformational Space [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (19 June 2009), e1000406. by Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck posted to beta-hairpin cmn dihedral free-energy hexapeptide short-peptides by Diego_Prada on 2009-06-19 10:09:14 as along with 4 people and 1 group physics phoenixzxl kshameer ppgardne Journal picks
	Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. [My Copy] Journal of the American Chemical Society, Vol. 130, No. 5. (6 February 2008), pp. 1538-1539. by C. Hyeon, D. Thirumalai posted to beta-hairpin free-energy pca protein_folding by Diego_Prada on 2009-06-15 16:05:55 as
	How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics? [My Copy] Physical Review Letters, Vol. 102, No. 23. (2009), 238102. by Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga posted to protein_dynamics pca funnels free-energy energy_landscape dpca by Diego_Prada on 2009-06-15 09:51:22 as along with 1 person agrossfield
	Energy landscape of a spin-glass model: Exploration and characterization [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 5. (2009), 051117. by Qing Zhou, Wing H. Wong posted to cmn complex_systems free-energy by Diego_Prada on 2009-06-06 17:10:38 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 cmn dialanine dihedral dpca entropy free-energy qha by Diego_Prada on 2009-06-03 11:08:23 as along with 2 people and 1 group anna_yershova sobolevnrm baker-group
	Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA [My Copy] SIAM Journal on Applied Dynamical Systems, Vol. 7, No. 2. (2008), pp. 532-560. by Illia Horenko, Evelyn Dittmer, Filip Lankas, John Maddocks, Philipp Metzner, Christof Schütte posted to cmn free-energy markov by Diego_Prada on 2009-05-30 20:53:56 as along with 1 person Elena_Zubova
	Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States [My Copy] Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1 (2006), pp. 495-517. by E. Meerbach, E. Dittmer, I. Horenko, C. Schütte posted to ala5 cmn free-energy hexapeptide short-peptides by Diego_Prada on 2009-05-30 20:42:39 as
	Two-state protein folding kinetics through all-atom molecular dynamics based sampling. [My Copy] Frontiers in bioscience : a journal and virtual library, Vol. 14 (2009), pp. 2801-2828. by P. G. Bolhuis posted to free-energy md protein_dynamics by Diego_Prada on 2009-05-30 19:31:01 as
	An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations [My Copy] Multiscale Modeling & Simulation, Vol. 2, No. 3. (2004), pp. 501-526. by Christof Schütte, Jessika Walter, Carsten Hartmann, Wilhelm Huisinga posted to cmn free-energy markov stochastic_processes struct_decorr by Diego_Prada on 2009-05-29 18:19:26 as
	A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo [My Copy] Journal of Computational Physics, Vol. 151 (May 1999), pp. 146-168. by Christof Schütte, Alexander Fischer, Wilhelm Huisinga, Peter Deuflhard posted to cmn complex_systems free-energy mc by Diego_Prada on 2009-05-16 17:05:37 as
	Energy Landscapes: From Clusters to Biomolecules [My Copy] Advances in Chemical Physics, Vol. 115 (2000), pp. 1-111. by David J. Wales, Jonathan P. Doye, Mark A. Miller, Paul N. Mortenson, Tiffany R. Walsh edited by I. Prigogine, Stuart A. Rice posted to chapt_cmn complex_systems free-energy plos by Diego_Prada on 2009-05-05 16:07:19 as
	Energy Landscapes : Applications to Clusters, Biomolecules and Glasses (Cambridge Molecular Science) [My Copy] (22 January 2004) by David Wales posted to complex_systems free-energy by Diego_Prada on 2009-05-05 15:45:30 as along with 3 people mtw hsekiguc alexispaz
	Folding Pathways and Rates for the Three-Stranded β-Sheet Peptide Beta3s using Discrete Path Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 29. (1 July 2008), pp. 8760-8769. by Joanne M. Carr, David J. Wales posted to beta-hairpin free-energy hexapeptide protein_folding short-peptides by Diego_Prada on 2009-04-30 12:10:50 as
	THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 1011-1021. by Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman posted to free-energy md md_history methods statistical_mechanics stochastic_processes by Diego_Prada on 2009-04-05 18:20:54 as along with 11 people and 1 group jrperillaj edws stephenbond dfgreen A_Coletta_Thesis sunnytov dgront sikorski jwagoner bransfop allmensch Structural Biology Group TorVergata
	Nonequilibrium Equality for Free Energy Differences [My Copy] Physical Review Letters, Vol. 78, No. 14. (7 April 1997), 2690. by C. Jarzynski posted to free-energy md_history out_of_equilibrium by Diego_Prada on 2009-04-05 17:29:27 as along with 4 people bosun cjryan hadesnumb samjlord
	Dynamical theory of activated processes in globular proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 79, No. 13. (July 1982), pp. 4035-4039. by S. H. Northrup, M. R. Pear, C. Y. Lee, J. A. Mccammon, M. Karplus posted to free-energy md md_history by Diego_Prada on 2009-04-05 17:10:15 as
	Diffusive reaction dynamics on invariant free energy profiles [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 37. (16 September 2008), pp. 13841-13846. by Sergei V. Krivov, Martin Karplus posted to articulo free-energy by Diego_Prada on 2009-03-21 17:44:16 as
	Algorithmic dimensionality reduction for molecular structure analysis [My Copy] The Journal of Chemical Physics, Vol. 129, No. 6. (2008), 064118. by Michael W. Brown, Shawn Martin, Sara N. Pollock, Evangelos A. Coutsias, Jean P. Watson posted to articulo free-energy pca by Diego_Prada on 2009-03-21 17:16:01 as
	Likelihood-Based Estimation of Multidimensional Langevin Models and Its Application to Biomolecular Dynamics [My Copy] Multiscale Modeling & Simulation, Vol. 7, No. 2. (2008), pp. 731-773. by Illia Horenko, Christof Schütte posted to free-energy langevin short-peptides statistical_mechanics stochastic_processes by Diego_Prada on 2009-03-07 12:46:38 as along with 1 person gardenes
	Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide [My Copy] Chemical Physics Letters, Vol. 466, No. 4-6. (04 December 2008), pp. 105-115. by Birgit Strodel, David J. Wales posted to amino articulo coarse-grained dialanine free-energy hexapeptide statistical_mechanics by Diego_Prada on 2009-03-07 12:18:52 as
	Absolute free energies estimated by combining pre-calculated molecular fragment libraries [My Copy] (30 Jan 2009) by Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman posted to coarse-grained dialanine free-energy short-peptides by Diego_Prada on 2009-03-04 12:12:11 as
	Foldamer dynamics expressed via Markov state models. II. State space decomposition [My Copy] The Journal of Chemical Physics, Vol. 123, No. 11. (2005) by Sidney P. Elmer, Sanghyun Park, Vijay S. Pande posted to free-energy markov short-peptides stochastic_processes by Diego_Prada on 2009-03-03 12:09:47 as
	Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water [My Copy] The Journal of Chemical Physics, Vol. 123, No. 11. (2005) by Sidney P. Elmer, Sanghyun Park, Vijay S. Pande posted to free-energy markov short-peptides stochastic_processes by Diego_Prada on 2009-03-03 12:06:39 as along with 1 person toerst
	The free energy landscape and dynamics of met-enkephalin [My Copy] The Journal of Chemical Physics, Vol. 119, No. 18. (2003), pp. 9947-9955. by David A. Evans, David J. Wales posted to chapt_cmn free-energy hexapeptide markov plos by Diego_Prada on 2009-02-17 15:55:06 as
	Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory [My Copy] J. Phys. Chem. B, Vol. 108, No. 21. (27 May 2004), pp. 6571-6581. by W. C. Swope, J. W. Pitera, F. Suits posted to chapt_cmn free-energy markov md plos protein_dynamics stochastic_processes by Diego_Prada on 2009-02-16 11:14:57 as along with 2 people mtw apaydin
	Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis [My Copy] The Journal of Chemical Physics, Vol. 128, No. 24. (2008) by Alexandros Altis, Moritz Otten, Phuong H. Nguyen, Rainer Hegger, Gerhard Stock posted to articulo dpca free-energy hexapeptide pca by Diego_Prada on 2008-12-16 11:16:42 as along with 2 people scampos agrossfield

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free-energy	93
networks	66
short-peptides	63
chapt_cmn	62
hexapeptide	48
plos	47
md	41
communities	38
markov	35
stochastic_processes	34
gnm	32
cmn	31
pca	30
protein_dynamics	29
protein_folding	28
amino	27
amyloids	27
dialanine	26
md_history	26
articulo	21
complex_systems	21
coarse-grained	18
beta-hairpin	16
hp_model	16
dpca	15
methods	15
proteins	15
transition_path	13
water	13
chapt_amino	12
force-fields	12
statistical_mechanics	12
transition_states	9
clustering	8
experimental	8
first_passage	8
markov_state_models	7
reaction_paths	7
active_site	6
glass_transition	6
mutual-information	6
rmsd	6
secondary_structure	6
struct_decorr	6
collective_motions	5
glycine	5
hot	5
kramers	5
langevin	5
mios	5
out_of_equilibrium	5
sampling	5
allostery	4
entropy	4
kinetic_models	4
mc	4
percolation	4
qha	4
dihedral	3
energy_landscape	3
rol_nodes	3
work_theorem	3
ala5	2
alanine	2
bayesian_analysis	2
conformational_entropy	2
fca	2
funnels	2
go	2
information	2
irreversibility	2
lanvegin	2
leas_action	2
non_markovian	2
probability_distributions	2
statistics	2
wavelets	2
aggregation	1
chain_interactions	1
discrete_breathers	1
enkaphalin	1
fibril_formation	1
flagellum	1
fre	1
hurst_exponent	1
information_theory	1
latex	1
mpi	1
nmr	1
nonequilibrium	1
opls	1
pendiente	1
protein_flexibility	1
relaxation_processes	1
review	1
statistical_models	1
t_dependence	1
temperature_dependence	1

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