Diego_Prada's library 486 articles Export

	Translational, rotational and internal dynamics of amyloid beta-peptides (A beta 40 and A beta 42) from molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 131, No. 15. (2009), 155103. by Ram P. Bora, Rajeev Prabhakar posted to amyloids by Diego_Prada on 2009-11-20 15:21:00 as
	Power-law distributions in empirical data [My Copy] (2 Feb 2009) by Aaron Clauset, Cosma R. Shalizi, M. E. J. Newman posted to probability_distributions by Diego_Prada on 2009-11-19 20:20:10 as along with 61 people and 2 groups kinop jaia lehalle jsaramak ccthomas vagoskar acrmartins krisl makrehchi jotwin quianominorleo akuhn arsyed coccoinomane janpaniev pawelsobko alexv Borelli tmarscha dpf garyfeng kubyaddi tnhh kaarsinogen dmeister ddahlem vtraag mattjb jfelipe yonyoni laurobeltrao mmcgloho galyardt gconaldi egh ansobol lfriedl jjray itmeson dumpa madhadron sdvillal bigbossman merazzle xpontus muraken sugarexpletive jaspervoskuilen tomhebbron gi0rgi0ne amoebe jasonn pprett AbnerCYH halukbingol anhlc stringertheory deanmalmgren jyew nazareno diamantis ReadingLab EntrepreneurialRisks
	Log-normal Distributions across the Sciences: Keys and Clues [My Copy] BioScience, Vol. 51, No. 5. (1 May 2001), pp. 341-352. by E. Limpert, W. A. Stahel, M. Abbt posted to probability_distributions by Diego_Prada on 2009-11-19 20:18:08 as along with 14 people and 3 groups rcrane bertelsen Kovanen fornstar karbak ansobol garyfeng ChaTo dfrankow harperf metamerist rubendrr feenstra kgajos ReadingLab GroupLens cytoskeleton-and-afm
	Characterization of Protein Conformational States by Normal-Mode Frequencies [My Copy] J. Am. Chem. Soc. (23 August 2007) by B. A. Hall, S. L. Kaye, A. Pang, R. Perera, P. C. Biggin posted to gnm by Diego_Prada on 2009-11-19 20:10:39 as along with 7 people and 3 groups Scis0000002 ubcg08l barry aqeel choonpeng sobolevnrm LamBras structural_bioinformatics Bioinformatics baker-group
	Estimating the sampling error: Distribution of transition matrices and functions of transition matrices for given trajectory data [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 2. (2009), 021106. by Philipp Metzner, Frank Noé, Christof Schütte posted to transition_states sampling markov_state_models by Diego_Prada on 2009-11-19 19:58:42 as along with 1 person agrossfield
	Progress and challenges in the automated construction of Markov state models for full protein systems [My Copy] The Journal of Chemical Physics, Vol. 131, No. 12. (2009), 124101. by Gregory R. Bowman, Kyle A. Beauchamp, George Boxer, Vijay S. Pande posted to sampling markov_state_models by Diego_Prada on 2009-11-19 19:52:24 as along with 1 person dlimmer
	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
	Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 19011-19016. by Frank NoÃ©, Christof SchÃ¼tte, Eric Vanden-Eijnden, Lothar Reich, Thomas R. Weikl posted to sampling markov_state_models by Diego_Prada on 2009-11-19 18:00:38 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
	The Structure and Function of Complex Networks [My Copy] SIAM Review, Vol. 45, No. 2. (2003), 167. by M. E. J. Newman posted to plos networks complex_systems chapt_cmn by Diego_Prada on 2009-11-18 19:00:31 as
	Community Structure in Directed Networks [My Copy] Physical Review Letters, Vol. 100, No. 11. (2008), 118703. by E. A. Leicht, M. E. J. Newman posted to networks communities chapt_cmn by Diego_Prada on 2009-11-18 18:16:29 as along with 7 people adamgyenge vtraag kubyaddi cgaugain cfelipesp Borelli orahcio
	Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 10. (13 May 2003), pp. 5742-5747. by Franc Avbelj, Robert L. Baldwin posted to short-peptides secondary_structure amino by Diego_Prada on 2009-11-18 16:36:07 as
	Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding [My Copy] Vol. 97, No. 8. (21 October 2009), pp. 2338-2347. by Peter L. Freddolino, Klaus Schulten posted to protein_folding by Diego_Prada on 2009-11-18 16:31:47 as
	A discussion of the solution for the best rotation to relate two sets of vectors [My Copy] Acta Cryst. A, Vol. 34 (1978), pp. 827-828. by W. Kabsch posted to rmsd methods by Diego_Prada on 2009-11-18 16:19:01 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
	Structural flexibility in proteins: impact of the crystal environment [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 521-528. by Konrad Hinsen posted to gnm by Diego_Prada on 2009-11-14 19:12:32 as along with 5 people and 2 groups mijogiffin barry sobolevnrm jlh64 scienbox baker-group McCammon
	Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian☆ [My Copy] Biophysical Journal, Vol. 93, No. 10. (15 November 2007), pp. 3460-3469. by K. Moritsugu, J. Smith posted to temperature_dependence gnm by Diego_Prada on 2009-11-14 19:09:10 as along with 4 people and 1 group aqeel hmk sobolevnrm choonpeng baker-group
	Application of Elastic Network Models to Proteins in the Crystalline State [My Copy] Vol. 96, No. 2. (21 January 2009), pp. 464-475. by Demian Riccardi, Qiang Cui, George N. Phillips posted to gnm collective_motions by Diego_Prada on 2009-11-14 19:00:21 as
	Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure [My Copy] Vol. 97, No. 9. (4 November 2009), pp. 2541-2549. by Hannes H. Loeffler, Akio Kitao posted to pca collective_motions by Diego_Prada on 2009-11-14 18:53:17 as along with 1 person agrossfield
	Harmonicity in slow protein dynamics [My Copy] Chemical Physics, Vol. 261, No. 1-2. (1 November 2000), pp. 25-37. by K. Hinsen, A. J. Petrescu, S. Dellerue, M. C. Bellissent-Funel, G. R. Kneller posted to gnm by Diego_Prada on 2009-11-14 18:46:39 as along with 4 people and 1 group abovell apaydin sobolevnrm saravan baker-group
	Protein elastic network models and the ranges of cooperativity [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 30. (28 July 2009), pp. 12347-12352. by Lei Yang, Guang Song, Robert L. Jernigan posted to gnm conformational_entropy by Diego_Prada on 2009-11-14 18:38:45 as along with 4 people anuragsethi sobolevnrm apaydin edws
	Physical arguments for distance-weighted interactions in elastic network models for proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. E128-E128. by Konrad Hinsen posted to gnm by Diego_Prada on 2009-11-14 18:28:40 as along with 1 person apaydin
	Graph clustering by flow simulation [My Copy] (2000) by S. van Dongen posted to networks communities chapt_cmn by Diego_Prada on 2009-11-02 20:32:11 as
	Funnels in energy landscapes [My Copy] The European Physical Journal B - Condensed Matter and Complex Systems, Vol. 63, No. 3. (1 June 2008), pp. 387-391. by K. Klemm, C. Flamm, P. F. Stadler posted to funnels energy_landscape by Diego_Prada on 2009-10-20 19:42:52 as
	The HP model of protein folding: A challenging testing ground for Wang–Landau sampling [My Copy] Computer Physics Communications, Vol. 179, No. 1-3. (July 2008), pp. 124-127. by T. Wust, D. Landau posted to hp_model by Diego_Prada on 2009-10-20 19:39:03 as along with 1 person flbarroso
	Exploring the lower part of discrete polymer model energy landscapes [My Copy] EPL (Europhysics Letters), Vol. 74, No. 4. (2006), pp. 726-732. by Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler posted to hp_model energy_landscape by Diego_Prada on 2009-10-20 19:34:16 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 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
	Math mode [My Copy] by Herbert Voss posted to latex by Diego_Prada on 2009-10-05 16:00:07 as
	Some notes on Force Fields: An Overview [My Copy] (14 February 2007) by Erik Marklund posted to force-fields by Diego_Prada on 2009-10-05 15:42:02 as
	What is principal component analysis? [My Copy] Nature biotechnology, Vol. 26, No. 3. (March 2008), pp. 303-304. by Markus Ringnér posted to pca clustering by Diego_Prada on 2009-09-19 15:58:18 as along with 67 people and 3 groups tnhh ruvido ucbcjbm daforerog abellogin nguizard thegoose2 arsyed Zephyrus flips svozil VGreiff kaniko ssgong Yanno guhjy operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu rsantana sobolevnrm fryanpan kengg rvosa dekay23 adacier hpaces waghsk rchauhan pavanghatty kristgy jfr bibay2004 xingxu quianominorleo craigwilson06 ashko markusd dayjm dimka i-stevenson chrissp100 tharris ale mjoach HugoMarcelo jdiezperezj rrbarb Nici baker-group FAB-lab Bioinformatics
	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
	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
	Discrete breathers in protein structures [My Copy] Physical Biology, Vol. 5, No. 2. (21 June 2008), 026001. by Francesco Piazza, Yves-Henri Sanejouand posted to networks gnm discrete_breathers allostery active_site by Diego_Prada on 2009-09-17 18:17:02 as along with 2 people sanejouand joseph_x_zhou
	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
	Creative elements: network-based predictions of active centres in proteins and cellular and social networks [My Copy] Trends in Biochemical Sciences, Vol. 33, No. 12. (20 December 2008), pp. 569-576. by P. Csermely posted to networks active_site by Diego_Prada on 2009-09-17 18:00:05 as along with 6 people and 1 group abhishek_tiwari sg45653 grahamc nilanjanroy cmmorel barry Bioinformatics
	Network Analysis of Protein Structures Identifies Functional Residues [My Copy] Journal of Molecular Biology, Vol. 344, No. 4. (03 December 2004), pp. 1135-1146. by Gil Amitai, Arye Shemesh, Einat Sitbon, et al.Maxim Shklar, Dvir Netanely, Ilya Venger, Shmuel Pietrokovski posted to networks gnm active_site by Diego_Prada on 2009-09-17 17:52:49 as along with 8 people and 1 group chrn vavi bicko Einat amitai sriram_s massivemayhem siebertm structural_bioinformatics
	Allosteric regulation and catalysis emerge via a common route [My Copy] Nature Chemical Biology, Vol. 4, No. 8. (18 July 2008), pp. 474-482. by Nina M. Goodey, Stephen J. Benkovic posted to allostery by Diego_Prada on 2009-09-17 17:50:05 as along with 3 people pablocarb barry paulschlesinger
	Gradient networks [My Copy] Journal of Physics A: Mathematical and Theoretical, Vol. 41, No. 15. (2008), 155103. by Zoltan Toroczkai, Balazs Kozma, Kevin E. Bassler, N. W. Hengartner, G. Korniss posted to networks by Diego_Prada on 2009-09-17 17:42:05 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

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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

Diego_Prada's library 486 articles Export

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