Diego_Prada's chapt_cmn [63 articles] Export

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	Targeted molecular dynamics: A new approach for searching pathways of conformational transitions [My Copy] Journal of Molecular Graphics, Vol. 12, No. 2. (June 1994), pp. 84-89. by J. Schlitter, M. Engels, P. Krüger posted to transition_path reaction_paths problems_fel_dof methods chapt_cmn by Diego_Prada on 2009-11-24 17:52:14 as along with 2 people cactus LamBras
	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
	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
	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
	Extracting macroscopic stochastic dynamics: Model problems [My Copy] Communications on Pure and Applied Mathematics, Vol. 56, No. 2. (2003), pp. 234-269. by Wilhelm Huisinga, Christof Schütte, Andrew M. Stuart posted to stochastic_processes non_markovian markov coarse-grained chapt_cmn by Diego_Prada on 2009-03-09 17:53:37 as
	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
	Finding communities in linear time: a physics approach [My Copy] The European Physical Journal B - Condensed Matter and Complex Systems, Vol. 38, No. 2. (25 March 2004), pp. 331-338. by F. Wu, B. A. Huberman posted to chapt_cmn communities networks by Diego_Prada on 2008-08-16 12:57:54 as along with 1 person birukou
	Fast algorithm for detecting community structure in networks [My Copy] Physical Review E, Vol. 69, No. 6. (Jun 2004), 066133. by M. E. J. Newman posted to chapt_cmn communities networks by Diego_Prada on 2008-08-16 12:23:31 as along with 6 people Shirakawa muraken cgaugain tnhh RobMills pdlug
	Defining and identifying communities in networks [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 9. (2 March 2004), pp. 2658-2663. by Filippo Radicchi, Claudio Castellano, Federico Cecconi, Vittorio Loreto, Domenico Parisi posted to chapt_cmn communities networks by Diego_Prada on 2008-08-15 19:06:40 as along with 19 people and 2 groups akavipat mussi almadana christiand vtraag kremso kubyaddi fabianavernero haewoon castellano shivaram jfr yas merazzle gcalda ltabourier sparikh carlk tnhh smc-infm T_lab
	Detecting network communities: a new systematic and efficient algorithm [My Copy] Journal of Statistical Mechanics: Theory and Experiment, Vol. 2004, No. 10. (2004) by Luca Donetti, Miguel posted to chapt_cmn communities networks by Diego_Prada on 2008-08-15 19:01:49 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
	GROMACS: fast, flexible, and free. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. Berendsen posted to chapt_cmn md by Diego_Prada on 2008-08-01 18:26:15 as along with 20 people and 2 groups arifor krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov A_Coletta_Thesis Radiation_Damage Stressosome
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to chapt_cmn md water by Diego_Prada on 2008-08-01 18:05:06 as along with 17 people and 1 group jmparks fralium bmduggan kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty CMB
	Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids [My Copy] Journal of the American Chemical Society, Vol. 118, No. 45. (1 January 1996), pp. 11225-11236. by William L. Jorgensen, David S. Maxwell, Julian Tirado-Rives posted to chapt_cmn force-fields md opls by Diego_Prada on 2008-08-01 17:47:35 as along with 9 people dimka snichols15 flbarroso tovrstra dfgreen sunnytov BragilMassoud loison softsimu
	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

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free-energy	94
networks	66
chapt_cmn	63
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	19
coarse-grained	18
methods	18
beta-hairpin	16
hp_model	16
dpca	15
proteins	15
force-fields	13
water	13
chapt_amino	12
statistical_mechanics	12
reaction_paths	10
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 chapt_cmn [63 articles] Export

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