Diego_Prada's plos [47 articles] Export

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	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
	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
	SYSTEMS BIOLOGY: Life's Complexity Pyramid [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 763-764. by Zoltan N. Oltvai, Albert-Laszlo Barabasi posted to chapt_cmn complex_systems plos by Diego_Prada on 2009-05-05 15:27:14 as along with 13 people and 6 groups joschaschmiedt navigators tomhebbron Scis0000002 agomez eldan yas wnpx sameetmehta jwdietrich mattjb franklin Ema MathBio Cybernetics ComplexAdaptiveSystems DSTO-CAS Biomedical_Cybernetics AQUA-FONTIS-Study
	Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains [My Copy] Linear Algebra and its Applications, Vol. 315, No. 1-3. (15 August 2000), pp. 39-59. by P. Deuflhard, W. Huisinga, A. Fischer, Ch Schütte posted to chapt_cmn markov plos by Diego_Prada on 2009-03-05 10:53:56 as
	Testing lumpability in Markov chains [My Copy] Statistics & Probability Letters, Vol. 64, No. 1. (01 August 2003), pp. 17-23. by R. W. Jernigan, R. H. Baran posted to chapt_cmn markov plos statistical_mechanics stochastic_processes by Diego_Prada on 2009-02-19 19:03:03 as
	Validation of Markov state models using Shannon's entropy [My Copy] The Journal of Chemical Physics, Vol. 124, No. 5. (2006) by Sanghyun Park, Vijay S. Pande posted to chapt_cmn entropy markov plos stochastic_processes by Diego_Prada on 2009-02-19 18:23:05 as along with 1 person toerst
	Nonequilibrium Statistical Mechanics [My Copy] (26 March 2001) by Robert Zwanzig posted to chapt_cmn markov plos statistical_mechanics by Diego_Prada on 2009-02-19 11:00:14 as along with 3 people NitinCR chiufanlee kkims
	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
	Remarks on non-Markov processes [My Copy] BRAZILIAN JOURNAL OF PHYSICS, Vol. 28, No. 2. (1998) by N. G. van Kampen posted to chapt_cmn langevin markov plos stochastic_processes by Diego_Prada on 2009-02-13 11:52:05 as
	Stochastic Processes in Physics and Chemistry (North-Holland Personal Library) [My Copy] (01 July 2001) by N. G. van Kampen posted to chapt_cmn kramers langevin markov plos statistical_mechanics stochastic_processes by Diego_Prada on 2009-02-13 11:41:48 as along with 2 people ddcttrl madhadron
	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
	From classical dynamics to continuous time random walks [My Copy] Journal of Statistical Physics, Vol. 30, No. 2. (1 February 1983), pp. 255-262. by Robert Zwanzig posted to chapt_cmn pendiente plos by Diego_Prada on 2009-02-11 17:08:20 as
	Coarse Master Equations for Peptide Folding Dynamics [My Copy] J. Phys. Chem. B (31 January 2008) by N. V. Buchete, G. Hummer posted to chapt_cmn hexapeptide markov plos stochastic_processes by Diego_Prada on 2008-12-16 16:27:49 as along with 3 people and 1 group apaydin ruvido sobolevnrm baker-group
	Reaction-rate theory: fifty years after Kramers [My Copy] Reviews of Modern Physics, Vol. 62, No. 2. (Apr 1990), pp. 251-341. by Peter Hänggi, Peter Talkner, Michal Borkovec posted to chapt_cmn kramers plos by Diego_Prada on 2008-11-28 19:18:58 as along with 9 people biblioteca_babel devinli sunrise chiufanlee yofar and_ped10 gi0rgi0ne ibschwartz dherkova
	Geometric versus topological clustering: an insight into conformation mapping. [My Copy] Proteins, Vol. 27, No. 2. (February 1997), pp. 213-226. by O. M. Becker posted to chapt_cmn free-energy hexapeptide plos by Diego_Prada on 2008-08-19 18:55:05 as
	Theory of protein folding. [My Copy] Current opinion in structural biology, Vol. 14, No. 1. (February 2004), pp. 70-75. by José Nelson N. Onuchic, Peter G. Wolynes posted to chapt_cmn plos protein_folding by Diego_Prada on 2008-08-16 19:39:29 as along with 6 people siggi84 flbarroso dgront choonpeng rabio allmensch
	Navigating the folding routes. [My Copy] Science (New York, N.Y.), Vol. 267, No. 5204. (17 March 1995), pp. 1619-1620. by P. G. Wolynes, J. N. Onuchic, D. Thirumalai posted to chapt_cmn plos protein_folding by Diego_Prada on 2008-08-16 19:31:06 as
	Comparing community structure identification [My Copy] Journal of Statistical Mechanics: Theory and Experiment, Vol. 2005, No. 09. (September 2005), pp. P09008-P09008. by Leon Danon, Albert Diaz-Guilera, Jordi Duch, Alex Arenas posted to chapt_cmn communities networks plos by Diego_Prada on 2008-08-15 17:59:14 as along with 8 people AaronMcDaid compbio krisl almadana Kovanen cgaugain conradlee dpf
	On the Structural Convergence of Biomolecular Simulations by Determination of the Effective Sample Size [My Copy] J. Phys. Chem. B (13 October 2007) by E. Lyman, D. M. Zuckerman posted to chapt_cmn plos struct_decorr by Diego_Prada on 2008-08-15 17:35:32 as along with 1 person and 1 group sobolevnrm baker-group
	Percolation and cluster distribution. I. Cluster multiple labeling technique and critical concentration algorithm [My Copy] Physical Review B, Vol. 14, No. 8. (15 October 1976), 3438. by J. Hoshen, R. Kopelman posted to chapt_cmn methods networks percolation plos by Diego_Prada on 2008-08-15 17:08:33 as along with 1 person alexphys
	Complex networks: Structure and dynamics [My Copy] Physics Reports, Vol. 424, No. 4-5. (February 2006), pp. 175-308. by S. Boccaletti, V. Latora, Y. Moreno, M. Chavez, D. Hwang posted to chapt_cmn networks plos by Diego_Prada on 2008-08-13 17:13:46 as along with 39 people and 2 groups Sergey_gerbek Katieleonard tessonec heitzig-j jotwin dschafer yizhi hendysh vtraag janpaniev fierykylin acrmartins kshundyak kubyaddi ocs anphony panisson lfriedl jmenche tjpp ansobol jrw BarrosH afragop craigtalbert merazzle kevinweil gennaro muraken hariprasadt jaspervoskuilen flavian_vasile ltabourier salvoscellato watson nolodie khloudi ebalp spool complex networks Complex_Real_Networks
	Small-world networks and the conformation space of a short lattice polymer chain [My Copy] EPL (Europhysics Letters), Vol. 55, No. 4. (2001), pp. 594-600. by A. Scala, Nunes L. A. Amaral, M. Barthélémy posted to chapt_cmn hp_model networks plos by Diego_Prada on 2008-08-11 22:52:26 as
	Complexity in Biology [My Copy] (5 Dec 1994) by Giorgio Parisi posted to chapt_cmn complex_systems plos by Diego_Prada on 2008-08-10 21:28:24 as
	Complex systems [My Copy] AIChE Journal, Vol. 49, No. 2. (2003), pp. 292-299. by J. M. Ottino posted to chapt_cmn complex_systems plos by Diego_Prada on 2008-08-10 19:19:12 as
	Complex systems and networks: challenges and opportunities for chemical and biological engineers [My Copy] Chemical Engineering Science In Complex Systems and Multi-scale Methodology, Vol. 59, No. 8-9. ( 2004), pp. 1653-1666. by L. A. N. Amaral, J. M. Ottino posted to chapt_cmn complex_systems networks plos by Diego_Prada on 2008-08-10 19:05:43 as
	A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. [My Copy] Journal of biomolecular structure & dynamics, Vol. 7, No. 3. (December 1989), pp. 421-453. by I. K. Roterman, M. H. Lambert, K. D. Gibson, H. A. Scheraga posted to chapt_cmn alanine amino dialanine plos by Diego_Prada on 2008-08-03 18:21:35 as
	Solvation - molecular-dynamics study of a dipeptide in water [My Copy] J. Am. Chem. Soc., Vol. 101, No. 8. (1979), pp. 1913-1937. by P. J. Rossky, M. Karplus posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-03 16:10:28 as
	The alanine dipeptide free energy surface in solution [My Copy] J. Chem. Phys., Vol. 111 (September 1999), pp. 5568-5579. by P. E. Smith posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-03 11:24:04 as
	Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models [My Copy] J. Phys. Chem. B, Vol. 108, No. 50. (16 December 2004), pp. 19487-19495. by D. S. Chekmarev, T. Ishida, R. M. Levy posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 19:46:15 as
	Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations [My Copy] J. Chem. Phys., Vol. 118 (June 2003), pp. 10762-10773. by G. Hummer, I. G. Kevrekidis posted to chapt_cmn coarse-grained dialanine md plos by Diego_Prada on 2008-08-01 19:40:41 as
	Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations [My Copy] Multiscale Modeling & Simulation, Vol. 5, No. 4. (2006), pp. 1214-1226. by John D. Chodera, William C. Swope, Jed W. Pitera, Ken A. Dill posted to chapt_cmn dialanine markov md plos by Diego_Prada on 2008-08-01 19:30:32 as along with 2 people allmensch ucbcjbm
	Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water [My Copy] The Journal of Chemical Physics, Vol. 110, No. 4. (1999), pp. 2099-2108. by Joannis Apostolakis, Philippe Ferrara, Amedeo Caflisch posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 19:00:45 as
	Automatic Method for Identifying Reaction Coordinates in Complex Systems [My Copy] J. Phys. Chem. B, Vol. 109, No. 14. (14 April 2005), pp. 6769-6779. by A. Ma, A. R. Dinner posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 18:54:53 as along with 2 people and 2 groups whitead A_Coletta_Thesis Jiang Research Group Structural Biology Group TorVergata
	Reaction coordinates of biomolecular isomerization. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 11. (23 May 2000), pp. 5877-5882. by P. G. Bolhuis, C. Dellago, D. Chandler posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 18:49:48 as along with 3 people stephenbond paddydu doktornoe
	NUMERICAL INTEGRATION OF STOCHASTIC DIFFERENTIAL EQUATIONS .2. [My Copy] BELL SYSTEM TECHNICAL JOURNAL, Vol. 60, No. 8. (1981) by H. S. Greenside, E. Helfand posted to chapt_cmn langevin methods plos by Diego_Prada on 2008-07-11 17:54:21 as
	Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels [My Copy] J. Phys. Chem. A, Vol. 106, No. 13. (4 April 2002), pp. 3213-3218. by R. Vargas, J. Garza, B. P. Hay, D. A. Dixon posted to chapt_cmn dialanine plos by Diego_Prada on 2008-05-07 15:38:46 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
	Graph transformation method for calculating waiting times in Markov chains [My Copy] The Journal of Chemical Physics, Vol. 124, No. 23. (2006) by Semen A. Trygubenko, David J. Wales posted to chapt_cmn free-energy markov plos by Diego_Prada on 2008-04-11 19:40:07 as along with 1 person apaydin
	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
	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
	Free energy disconnectivity graphs: Application to peptide models [My Copy] The Journal of Chemical Physics, Vol. 117, No. 23. (2002), pp. 10894-10903. by Sergei V. Krivov, Martin Karplus posted to chapt_cmn free-energy plos by Diego_Prada on 2008-02-19 10:28:36 as
	Hidden complexity of free energy surfaces for peptide (protein) folding. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 41. (12 October 2004), pp. 14766-14770. by S. V. Krivov, M. Karplus posted to chapt_cmn free-energy plos proteins by Diego_Prada on 2008-02-19 10:22:29 as along with 4 people apaydin dimka bilab Fernando_FF
	Energy landscapes: calculating pathways and rates [My Copy] International Reviews in Physical Chemistry, Vol. 25, No. 1-2. (2006), pp. 237-282. by David J. Wales posted to chapt_cmn free-energy kramers plos by Diego_Prada on 2008-02-17 13:20:49 as
	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
chapt_cmn	64
short-peptides	63
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
transition_path	20
methods	19
coarse-grained	18
beta-hairpin	16
hp_model	16
dpca	15
proteins	15
force-fields	13
water	13
chapt_amino	12
statistical_mechanics	12
reaction_paths	11
transition_states	10
clustering	8
experimental	8
first_passage	8
markov_state_models	7
problems_fel_dof	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
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 plos [47 articles] Export

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