Diego_Prada's protein_dynamics [29 articles] Export

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	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
	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2312-2334. by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham posted to protein_dynamics md communities clustering beta-hairpin by Diego_Prada on 2009-09-19 15:52:15 as along with 9 people and 3 groups anuragsethi scampos oteri barry daevans sobolevnrm LamBras allmensch GermanErlenkamp Structural Biology Group TorVergata structural_bioinformatics baker-group
	A hierarchy of timescales in protein dynamics is linked to enzyme catalysis [My Copy] Nature (18 November 2007) by Katherine A. Henzler-Wildman, Ming Lei, Vu Thai, Jordan S. Kerns, Martin Karplus, Dorothee Kern posted to struct_decorr proteins protein_dynamics collective_motions allostery active_site by Diego_Prada on 2009-09-19 15:45:21 as along with 9 people and 1 group ruvido tmmurali allmensch cactus sobolevnrm jlh64 RamuAnandakrishnan dmobley chenway baker-group
	Simultaneous determination of protein structure and dynamics [My Copy] Nature, Vol. 433, No. 7022. (13 January 2005), pp. 128-132. by Kresten Lindorff-Larsen, Robert B. Best, Mark A. Depristo, Christopher M. Dobson, Michele Vendruscolo posted to proteins protein_folding protein_dynamics by Diego_Prada on 2009-09-19 15:42:18 as along with 15 people and 3 groups xdeupi A_Coletta_Thesis karbak apaydin barry lillekatt baaden lna dgront allmensch daevans rsantana jlh64 biehl rph Structural Biology Group TorVergata 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 17 people and 1 group xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
	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
	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
	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
	Prediction of chain flexibility in proteins [My Copy] Naturwissenschaften, Vol. 72, No. 4. (1 April 1985), pp. 212-213. by P. A. Karplus, G. E. Schulz posted to gnm protein_dynamics protein_folding proteins by Diego_Prada on 2009-04-30 11:55:17 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
	termostato2 [My Copy] posted to md methods protein_dynamics by Diego_Prada on 2008-12-18 18:00:09 as
	Peptide Folding: When Simulation Meets Experiment [My Copy] Angewandte Chemie International Edition, Vol. 38, No. 1-2. (1999), pp. 236-240. by Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F. van Gunsteren, Alan E. Mark posted to beta-hairpin md protein_dynamics short-peptides by Diego_Prada on 2008-12-15 12:06:57 as along with 2 people dsmueller jteyra
	Dihedral angle principal component analysis of molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 126, No. 24. (2007) by Alexandros Altis, Phuong H. Nguyen, Rainer Hegger, Gerhard Stock posted to articulo dpca md pca protein_dynamics by Diego_Prada on 2008-09-24 11:39:38 as along with 4 people and 1 group scampos barry ruvido nh structural_bioinformatics
	Theory of Kinetic Partitioning in Protein Folding (With Application to Prions) [My Copy] (25 Jun 1996) by V. I. Abkevich, A. M. Gutin, E. I. Shakhnovich posted to protein_dynamics transition_path by Diego_Prada on 2008-08-11 21:58:28 as along with 1 person and 1 group maurizio_prion prionbiology
	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
	Annealed importance sampling of dileucine peptide [My Copy] (3 Apr 2007) by Edward Lyman, Daniel M. Zuckerman posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:15:40 as
	Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model [My Copy] (24 Mar 2007) by Marty F. Ytreberg, Svetlana, Daniel M. Zuckerman posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:13:08 as
	Network and graph analyses of folding free energy surfaces [My Copy] Current Opinion in Structural Biology In Protein-nucleic acid interactions/Folding and binding - Wei Yang and Gregory D Van Dyne/Mikael Oliveberg and Eugene I Shakhnovich, Vol. 16, No. 1. (February 2006), pp. 71-78. by Amedeo Caflisch posted to chapt_cmn free-energy plos protein_dynamics by Diego_Prada on 2008-04-11 19:59:28 as along with 5 people and 1 group barry apaydin bilab mtw jlh64 structural_bioinformatics
	Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. [My Copy] J Chem Phys, Vol. 126, No. 15. (21 April 2007) by F. Noé, I. Horenko, C. Schütte, J. C. Smith posted to chapt_cmn hexapeptide markov plos protein_dynamics by Diego_Prada on 2008-03-30 16:22:35 as along with 3 people barmak7282 choonpeng toerst
	Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 126, No. 24. (2007) by Nina S. Hinrichs, Vijay S. Pande posted to markov protein_dynamics by Diego_Prada on 2008-03-30 16:17:53 as
	Statistically optimal analysis of samples from multiple equilibrium states [My Copy] (9 Jan 2008) by Michael R. Shirts, John D. Chodera posted to markov protein_dynamics stochastic_processes by Diego_Prada on 2008-03-30 16:14:48 as along with 1 person and 1 group sobolevnrm baker-group
	Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics [My Copy] The Journal of Chemical Physics, Vol. 126, No. 15. (21 April 2007), 155101. by John D. Chodera, Nina Singhal, Vijay S. Pande, Ken A. Dill, William C. Swope posted to chapt_cmn markov plos protein_dynamics by Diego_Prada on 2008-03-30 16:13:45 as along with 2 people ruvido allmensch
	Exploration of the free-energy surface of a three-helix peptide with stochastic optimization methods [My Copy] International Journal of Quantum Chemistry, Vol. 99, No. 5. (2004), pp. 854-863. by T. Herges, A. Schug, W. Wenzel posted to free-energy protein_dynamics by Diego_Prada on 2008-02-19 10:19:16 as
	Free-energy landscape of the villin headpiece in an all-atom force field. [My Copy] Structure (Camb), Vol. 13, No. 4. (April 2005), pp. 661-668. by T. Herges, W. Wenzel posted to free-energy protein_dynamics by Diego_Prada on 2008-02-19 10:10:21 as along with 2 people nigham fjc1
	Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories [My Copy] Polymer, Vol. 43, No. 2. (January 2002), pp. 431-439. by Pemra Doruker, Ivet Bahar, Canan Baysal, Burak Erman posted to gnm pca protein_dynamics by Diego_Prada on 2008-02-18 17:48:28 as
	The structural de-correlation time: A robust statistical measure of convergence of biomolecular simulations [My Copy] (18 Feb 2007) by Edward Lyman, Daniel M. Zuckerman posted to protein_dynamics proteins struct_decorr by Diego_Prada on 2008-02-18 17:18:27 as
	Dynamics of essential collective motions in proteins: Theory [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 5. (2007) by Maria Stepanova posted to pca protein_dynamics proteins by Diego_Prada on 2008-02-17 12:43:10 as along with 2 people and 1 group choonpeng sobolevnrm baker-group

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free-energy	87
networks	66
short-peptides	62
chapt_cmn	61
hexapeptide	48
plos	47
md	41
communities	38
markov	35
stochastic_processes	34
cmn	29
pca	29
protein_dynamics	29
protein_folding	27
amino	26
amyloids	26
md_history	26
dialanine	25
gnm	25
articulo	21
complex_systems	21
coarse-grained	18
hp_model	16
beta-hairpin	15
dpca	15
proteins	15
methods	14
transition_path	13
water	13
chapt_amino	12
force-fields	12
statistical_mechanics	12
clustering	8
experimental	8
first_passage	8
reaction_paths	7
transition_states	7
active_site	6
glass_transition	6
mutual-information	6
struct_decorr	6
glycine	5
hot	5
kramers	5
langevin	5
mios	5
out_of_equilibrium	5
rmsd	5
secondary_structure	5
allostery	4
entropy	4
kinetic_models	4
mc	4
percolation	4
qha	4
collective_motions	3
dihedral	3
energy_landscape	3
rol_nodes	3
work_theorem	3
ala5	2
alanine	2
bayesian_analysis	2
fca	2
funnels	2
go	2
information	2
irreversibility	2
lanvegin	2
leas_action	2
non_markovian	2
statistics	2
wavelets	2
chain_interactions	1
conformational_entropy	1
discrete_breathers	1
enkaphalin	1
flagellum	1
hurst_exponent	1
information_theory	1
latex	1
markov_state_models	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

Diego_Prada's protein_dynamics [29 articles] Export

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