Diego_Prada's cmn [31 articles] Export

Recent papers added to Diego_Prada's library classified by the tag cmn. You can also see everyone's cmn.

	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
	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
	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
	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
	Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. [My Copy] Current protein & peptide science, Vol. 10, No. 2. (April 2009), pp. 161-172. by Miklós A. Antal, Csaba Böde, Peter Csermely posted to percolation networks cmn active_site by Diego_Prada on 2009-09-17 18:13:11 as
	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
	Thermodynamic functions of conformational changes: conformational network of glycine diamide folding, entropy lowering, and informational accumulation. [My Copy] The journal of physical chemistry. A, Vol. 110, No. 49. (14 December 2006), pp. 13325-13331. by Szilard N. Fejer, Imre G. Csizmadia, Bela Viskolcz posted to amino cmn glycine by Diego_Prada on 2009-08-04 11:17:45 as
	Multiscale complex network of protein conformational fluctuations in single-molecule time series [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 2. (15 January 2008), pp. 536-541. by Chun-Biu Li, Haw Yang, Tamiki Komatsuzaki posted to cmn markov out_of_equilibrium by Diego_Prada on 2009-07-21 15:16:32 as along with 5 people and 1 group victorclaessen ruvido sobolevnrm biehl hsekiguc baker-group
	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
	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
	From simulation data to conformational ensembles: Structure and dynamics-based methods [My Copy] Journal of Computational Chemistry, Vol. 20, No. 16. (1999), pp. 1760-1774. by Wilhelm Huisinga, Christoph Best, Rainer Roitzsch, Christof Schütte, Frank Cordes posted to clustering cmn pca by Diego_Prada on 2009-05-30 19:58:33 as along with 2 people welliegirl thegoose
	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
	Transition networks for modeling the kinetics of conformational change in macromolecules [My Copy] Current Opinion in Structural Biology In Theory and simulation / Macromolecular assemblages, Vol. 18, No. 2. (April 2008), pp. 154-162. by Frank Noé, Stefan Fischer posted to chapt_cmn cmn hexapeptide markov networks plos by Diego_Prada on 2009-02-11 18:08:45 as along with 5 people and 3 groups aqeel barry sobolevnrm paulschlesinger toerst structural_bioinformatics baker-group McCammon
	Simulating replica exchange simulations of protein folding with a kinetic network model [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15340-15345. by Weihua Zheng, Michael Andrec, Emilio Gallicchio, Ronald M. Levy posted to cmn markov md methods by Diego_Prada on 2008-11-29 15:56:08 as along with 1 person zwang
	Diffusion and networks: A powerful combination! [My Copy] (26 Aug 2005) by Ingve Simonsen posted to networks cmn by Diego_Prada on 2008-08-10 21:58:41 as
	Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems [My Copy] International Reviews in Physical Chemistry, Vol. 27, No. 2. (2008), pp. 201-227. by Yi Q. Gao, Lijiang Yang, Yubo Fan, Qiang Shao posted to complex_systems free-energy protein_dynamics transition_path cmn by Diego_Prada on 2008-08-10 20:26:43 as
	Network Topology of a Potential Energy Landscape: A Static Scale-Free Network [My Copy] Physical Review Letters, Vol. 88, No. 23. (20 May 2002), 238701. by Jonathan P. K. Doye posted to networks cmn by Diego_Prada on 2008-08-10 19:03:17 as along with 1 person poccian
	On mean residence and first passage times in finite one-dimensional systems [My Copy] The Journal of Chemical Physics, Vol. 109, No. 13. (1998), pp. 5187-5193. by Arie B. Haim, Joseph Klafter posted to markov stochastic_processes cmn by Diego_Prada on 2008-05-10 11:47:32 as
	Comparison of mode analyses at different resolutions applied to nucleic acid systems. [My Copy] Biophys J, Vol. 89, No. 5. (November 2005), pp. 2939-2949. by A. W. Van Wynsberghe, Q. Cui posted to coarse-grained gnm pca cmn by Diego_Prada on 2008-02-18 18:18:29 as along with 2 people aqeel eckart_bindewald
	Construction of effective free energy landscape from single-molecule time series [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302. by Akinori Baba, Tamiki Komatsuzaki posted to communities networks free-energy cmn by Diego_Prada on 2008-02-17 12:51:10 as along with 7 people and 1 group victorclaessen hmk zwang cactus sobolevnrm arnaudriegert hsekiguc baker-group
	Topographical complexity of multidimensional energy landscapes [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 49. (5 December 2006), pp. 18551-18555. by Gareth J. Rylance, Roy L. Johnston, Yasuhiro Matsunaga, Chun-Biu Li, Akinori Baba, Tamiki Komatsuzaki posted to communities networks free-energy cmn by Diego_Prada on 2008-02-17 12:50:10 as
	Network analysis of protein dynamics [My Copy] FEBS Letters, Vol. 581, No. 15. (19 June 2007), pp. 2776-2782. by C. Bode, I. Kovacs, M. Szalay, R. Palotai, T. Korcsmaros, P. Csermely posted to networks free-energy cmn by Diego_Prada on 2008-02-17 12:20:15 as along with 4 people mjbradle choonpeng george_g jlh64
	The protein folding network. [My Copy] J Mol Biol, Vol. 342, No. 1. (3 September 2004), pp. 299-306. by F. Rao, A. Caflisch posted to chapt_cmn cmn networks plos by Diego_Prada on 2008-02-17 12:18:38 as along with 6 people and 1 group camster apaydin allmensch ruvido jlh64 nh dbk-lab
	Uncovering the topology of configuration space networks [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 2. (2007) by David Gfeller, David M. de Lachapelle, Paolo, Guido Caldarelli, Francesco Rao posted to chapt_cmn cmn plos by Diego_Prada on 2008-02-17 12:17:16 as along with 3 people pdelosri jlh64 SMC
	From the Cover: Complex network analysis of free-energy landscapes [My Copy] PNAS, Vol. 104, No. 6. (6 February 2007), pp. 1817-1822. by D. Gfeller, De Los, A. Caflisch, F. Rao posted to chapt_cmn cmn communities free-energy networks plos by Diego_Prada on 2008-02-17 12:12:33 as along with 4 people noby jlh64 marcio nh

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free-energy	94
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
amino	28
protein_folding	28
amyloids	27
dialanine	27
md_history	26
articulo	21
complex_systems	21
coarse-grained	18
transition_path	17
beta-hairpin	16
hp_model	16
methods	16
dpca	15
proteins	15
force-fields	13
water	13
chapt_amino	12
statistical_mechanics	12
transition_states	10
clustering	8
experimental	8
first_passage	8
reaction_paths	8
markov_state_models	7
active_site	6
glass_transition	6
mutual-information	6
problems_fel_dof	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
alanine	3
dihedral	3
energy_landscape	3
rol_nodes	3
work_theorem	3
ala5	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

Diego_Prada's cmn [31 articles] Export

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