Diego_Prada's methods [27 articles] Export

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

	Computing time scales from reaction coordinates by milestoning [My Copy] The Journal of Chemical Physics, Vol. 120, No. 23. (2004), pp. 10880-10889. by Anton K. Faradjian, Ron Elber posted to transition_path reaction_paths methods by Diego_Prada on 2009-11-25 19:23:28 as along with 1 person apaydin
	Transition Path Sampling Methods [My Copy] Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1 (2006), pp. 349-391. by C. Dellago, P. G. Bolhuis, P. L. Geissler posted to transition_path sampling methods chapt_cmn by Diego_Prada on 2009-11-25 19:19:57 as
	TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark [My Copy] Annual Review of Physical Chemistry, Vol. 53, No. 1. (2002), pp. 291-318. by Peter G. Bolhuis, David Chandler, Christoph Dellago, Phillip L. Geissler posted to transition_path reaction_paths methods chapt_cmn by Diego_Prada on 2009-11-25 18:42:21 as along with 5 people doktornoe cjryan apaydin allmensch jun
	String method for the study of rare events [My Copy] Physical Review B, Vol. 66, No. 5. (12 Aug 2002), 052301. by E. Weinan, Weiqing Ren, Eric V. Eijnden posted to transition_path methods chapt_cmn by Diego_Prada on 2009-11-25 18:14:52 as along with 1 person hugo_yas
	Nudged elastic band method for finding minimum energy paths of transition [My Copy] In Classical and quantum dynamics in condensed phase simulations (1998), pp. 385-404. by H. Jónsson, G. Mills, K. W. Jacobsen posted to transition_path methods chapt_cmn by Diego_Prada on 2009-11-25 17:59:57 as
	Methods for Finding Saddle Points and Minimum Energy Paths [My Copy] Theoretical Methods in Condensed Phase Chemistry (2001), pp. 269-302. by Graeme Henkelman, Gísli Jóhannesson, Hannes Jónsson posted to transition_path methods by Diego_Prada on 2009-11-25 17:40:14 as
	First-principles calculation of the folding free energy of a three-helix bundle protein [My Copy] Science, Vol. 269, No. 5222. (21 July 1995), pp. 393-396. by E. M. Boczko, Cl Brooks posted to protein_folding methods by Diego_Prada on 2009-11-25 16:48:19 as
	FROM FOLDING THEORIES TO FOLDING PROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding [My Copy] Annual Review of Physical Chemistry, Vol. 52, No. 1. (2001), pp. 499-535. by Joan E. Shea, Charles L. Brooks posted to review protein_folding methods free-energy by Diego_Prada on 2009-11-25 16:26:15 as along with 3 people scampos fjc1 allmensch
	Structural mechanism of the recovery stroke in the Myosin molecular motor [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6873-6878. by Stefan Fischer, BjÃ¶rn WindshÃ¼gel, Daniel Horak, Kenneth C. Holmes, Jeremy C. Smith posted to transition_path reaction_paths methods chapt_cmn by Diego_Prada on 2009-11-25 12:29:13 as along with 4 people and 2 groups ckmyo barry shuns yalexeev structural_bioinformatics Bioinformatics
	Steered molecular dynamics and mechanical functions of proteins [My Copy] Current Opinion in Structural Biology, Vol. 11, No. 2. (1 April 2001), pp. 224-230. by B. Isralewitz, M. Gao, K. Schulten posted to transition_path reaction_paths methods by Diego_Prada on 2009-11-24 18:31:21 as along with 4 people and 2 groups devinli barry ttjoseph LamBras structural_bioinformatics Bioinformatics
	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
	Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom [My Copy] Chemical Physics Letters, Vol. 194, No. 3. (26 June 1992), pp. 252-261. by S. Fischer, M. Karplus posted to transition_path reaction_paths problems_fel_dof methods free-energy by Diego_Prada on 2009-11-23 17:38:17 as along with 1 person ckmyo
	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
	Multidimensional Langevin modeling of biomolecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 130, No. 3. (2009), 034106. by Rainer Hegger, Gerhard Stock posted to lanvegin md methods pca short-peptides by Diego_Prada on 2009-05-30 19:16:19 as along with 1 person and 1 group sobolevnrm baker-group
	Extracting macroscopic dynamics: model problems and algorithms [My Copy] Nonlinearity, Vol. 17, No. 6. (2004), pp. R55-R127. by Raz, Andrew Stuart posted to markov methods stochastic_processes by Diego_Prada on 2009-05-30 18:54:10 as along with 2 people and 1 group sobolevnrm Borelli baker-group
	Some methods for classification and analysis of multivariate observations [My Copy] In Fifth Berkeley Symposium on Mathematical Statistics and Probability (1967), pp. 281-297. by J. Macqueen edited by University posted to clustering methods by Diego_Prada on 2009-05-16 19:46:48 as along with 3 people mijam votis sugarexpletive
	The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition (Springer Series in Statistics) [My Copy] (15 September 2009) by Trevor Hastie, Robert Tibshirani, Jerome Friedman posted to clustering methods statistics by Diego_Prada on 2009-05-16 17:14:56 as along with 9 people pjmaybank robertlischke derwisch saus83 ilyashl ocs christofseiler matjes czeller
	HOW WELL CAN SIMULATION PREDICT PROTEIN FOLDING KINETICS AND THERMODYNAMICS? [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 34, No. 1. (29 October 2005), pp. 43-69. by Christopher D. Snow, Eric J. Sorin, Young M. Rhee, Vijay S. Pande posted to md methods protein_folding statistical_mechanics stochastic_processes by Diego_Prada on 2009-04-30 12:01:14 as along with 9 people amphibina flbarroso doktornoe dgront blackbart allmensch saunders evanse toerst
	THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 1011-1021. by Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman posted to free-energy md md_history methods statistical_mechanics stochastic_processes by Diego_Prada on 2009-04-05 18:20:54 as along with 11 people and 1 group jrperillaj edws stephenbond dfgreen A_Coletta_Thesis sunnytov dgront sikorski jwagoner bransfop allmensch Structural Biology Group TorVergata
	Replica-exchange molecular dynamics method for protein folding [My Copy] Chemical Physics Letters, Vol. 314, No. 1-2. (26 November 1999), pp. 141-151. by Y. Sugita posted to md md_history methods statistical_mechanics stochastic_processes by Diego_Prada on 2009-04-05 17:41:37 as along with 8 people and 1 group chemrahul82 tovrstra oteri Sylvain_Prigent andreasauerwein dgront allmensch rulix Structural Biology Group TorVergata
	termostato2 [My Copy] posted to md methods protein_dynamics by Diego_Prada on 2008-12-18 18:00:09 as
	Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 35. (1 September 2006), pp. 17616-17626. by Berk Hess, Nico F. A. van der Vegt posted to md methods by Diego_Prada on 2008-12-10 12:26:36 as along with 6 people and 1 group softsimu arnaucordomi krapnik flbarroso Marine ashaytan Molecular dynamics in MSU
	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
	Using quaternions to calculate RMSD. [My Copy] J Comput Chem, Vol. 25, No. 15. (30 November 2004), pp. 1849-1857. by E. A. Coutsias, C. Seok, K. A. Dill posted to articulo methods rmsd by Diego_Prada on 2008-09-26 18:09:36 as along with 6 people eskay BragilMassoud apaydin nachtalp dgront rabio
	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
	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
	Percolation and cluster structure parameters: The enhanced Hoshen-Kopelman algorithm [My Copy] Physical Review E, Vol. 56, No. 2. (1997), 1455. by J. Hoshen, M. W. Berry, K. S. Minser posted to communities methods networks percolation by Diego_Prada on 2008-02-17 12:34:58 as

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free-energy	98
chapt_cmn	71
networks	66
short-peptides	63
hexapeptide	48
plos	47
md	41
communities	38
markov	35
protein_folding	34
stochastic_processes	34
cmn	33
gnm	32
protein_dynamics	31
pca	30
amino	28
amyloids	27
dialanine	27
md_history	27
methods	27
transition_path	26
articulo	21
complex_systems	21
coarse-grained	18
beta-hairpin	16
hp_model	16
dpca	15
proteins	15
force-fields	13
reaction_paths	13
water	13
chapt_amino	12
statistical_mechanics	12
transition_states	12
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
sampling	6
secondary_structure	6
struct_decorr	6
collective_motions	5
glycine	5
hot	5
kramers	5
langevin	5
mios	5
out_of_equilibrium	5
review	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
statistical_models	1
t_dependence	1
temperature_dependence	1

Diego_Prada's methods [27 articles] Export

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