ruvido's watchlist [at least 200 articles] Export

Recent papers matching ruvido's watchlist criteria

	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
	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
	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
	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
	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
	Conformational entropy of alanine versus glycine in protein denatured states [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 8. (20 February 2007), pp. 2661-2666. by Kathryn A. Scott, Darwin O. V. Alonso, Satoshi Sato, Alan R. Fersht, Valerie Daggett posted to hexapeptide glycine free-energy conformational_entropy alanine by Diego_Prada on 2009-09-17 12:38:50 as
	From time series to complex networks: The visibility graph [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 13. (1 April 2008), pp. 4972-4975. by Lucas Lacasa, Bartolo Luque, Fernando Ballesteros, Jordi Luque, Juan C. NuÃ±o posted to networks by Diego_Prada on 2009-09-15 17:58:14 as along with 5 people Borelli ocs AbnerCYH biehl vrich
	The visibility graph: A new method for estimating the Hurst exponent of fractional Brownian motion [My Copy] EPL (Europhysics Letters), Vol. 86, No. 3. (2009), 30001. by L. Lacasa, B. Luque, J. Luque, J. C. Nuno posted to hurst_exponent by Diego_Prada on 2009-09-15 17:49:24 as
	New method to analyze simulations of activated processes [My Copy] The Journal of Chemical Physics, Vol. 126, No. 13. (2007), 134103. by Jan Wedekind, Reinhard Strey, David Reguera posted to stochastic_processes kinetic_models free-energy first_passage by Diego_Prada on 2009-09-15 17:23:41 as along with 1 person janw
	Kinetic Reconstruction of the Free-Energy Landscape [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 35. (4 September 2008), pp. 11060-11063. by Jan Wedekind, David Reguera posted to kinetic_models free-energy first_passage by Diego_Prada on 2009-09-15 17:21:40 as along with 3 people janwedekind paulschlesinger michaelbussmann
	Evaluating nucleation rates in direct simulations [My Copy] The Journal of Chemical Physics, Vol. 130, No. 6. (2009), 064505. by Guram Chkonia, Judith Wölk, Reinhard Strey, Jan Wedekind, David Reguera posted to first_passage by Diego_Prada on 2009-09-15 17:19:30 as along with 3 people mc1975 vitroid lutsko
	Sequence alignment and mutual information [My Copy] (23 Oct 2008) by Orion Penner, Peter Grassberger, Maya Paczuski posted to mutual-information by Diego_Prada on 2009-09-15 17:11:25 as along with 1 person jengeldk
	MIC: Mutual Information Based Hierarchical Clustering [My Copy] Information Theory and Statistical Learning (2009), pp. 101-123. by Alexander Kraskov, Peter Grassberger posted to mutual-information clustering by Diego_Prada on 2009-09-15 17:08:53 as
	Entropy production and the arrow of time [My Copy] New Journal of Physics, Vol. 11, No. 7. (2009), 073008. by J. M. R. Parrondo, Broeck, R. Kawai posted to work_theorem stochastic_processes irreversibility entropy by Diego_Prada on 2009-09-15 16:57:51 as along with 1 person pak
	The “footprints” of irreversibility [My Copy] EPL (Europhysics Letters), Vol. 82, No. 5. (2008), 50002. by A. Gomez-Marin, J. M. R. Parrondo, Broeck posted to work_theorem stochastic_processes irreversibility by Diego_Prada on 2009-09-15 16:51:09 as
	Dissipation: The Phase-Space Perspective [My Copy] Physical Review Letters, Vol. 98, No. 8. (2007), 080602. by R. Kawai, J. M. R. Parrondo, C. Van den Broeck posted to work_theorem stochastic_processes out_of_equilibrium free-energy by Diego_Prada on 2009-09-15 16:47:43 as along with 1 person madhadron
	Detection of Functional Modes in Protein Dynamics [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000480. by Jochen S. Hub, Bert L. de Groot posted to pca gnm collective_motions by Diego_Prada on 2009-09-04 09:14:56 as along with 3 people sobolevnrm klexa zwang
	Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (4 September 2009), e1000496. by Timothy R. Lezon, Andrej Sali, Ivet Bahar posted to gnm by Diego_Prada on 2009-09-04 09:12:27 as
	A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (7 August 2009), e1000452. by Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana posted to kinetic_models by Diego_Prada on 2009-08-31 17:40:25 as along with 2 people paddydu fabiopietrucci
	Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (14 August 2009), e1000470. by Mati Cohen, Vladimir Potapov, Gideon Schreiber posted to chain_interactions by Diego_Prada on 2009-08-31 17:38:47 as along with 6 people nickolay klexa zwang reyez TRHvidsten ericrpaquet
	Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms1 [My Copy] Journal of Molecular Biology, Vol. 285, No. 4. (29 January 1999), pp. 1711-1733. by Word, Simon C. Lovell, Thomas H. Labean, et al.Hope C. Taylor, Michael E. Zalis, Brent K. Presley, Jane S. Richardson, David C. Richardson posted to chapt_amino amino by Diego_Prada on 2009-08-12 12:21:51 as along with 4 people and 5 groups aqeel dgront barry joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	A survey of left-handed polyproline II helices [My Copy] Protein Science, Vol. 8, No. 3. (1999), pp. 587-595. by Benjamin J. Stapley, Trevor P. Creamer posted to chapt_amino amino by Diego_Prada on 2009-08-07 20:58:59 as
	In Vivo Chemical Modification of Proteins (Post-Translational Modification) [My Copy] Annual Review of Biochemistry, Vol. 50, No. 1. (1981), pp. 783-814. by F. Wold posted to amino by Diego_Prada on 2009-08-07 17:51:47 as
	Posttranslational covalent modification of proteins [My Copy] Science, Vol. 198, No. 4320. (2 December 1977), pp. 890-896. by R. Uy, F. Wold posted to amino by Diego_Prada on 2009-08-07 17:47:47 as
	Conformation of Polypeptides and Proteins [My Copy] In Advances in Protein Chemistry Volume 23, Vol. 23 (1968), pp. 283-437. by G. N. Ramachandran, V. Sasisekharan posted to chapt_amino amino by Diego_Prada on 2009-08-07 12:47:38 as
	Stereochemical quality of protein structure coordinates [My Copy] Proteins: Structure, Function, and Genetics, Vol. 12, No. 4. (3 February 1992), pp. 345-364. by Anne L. Morris, Malcolm W. Macarthur, E. Gail Hutchinson, Janet M. Thornton posted to chapt_amino amino by Diego_Prada on 2009-08-07 12:32:21 as along with 2 people aqeel andreasauerwein
	The Protein Data Bank [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 235-242. by Helen M. Berman, John Westbrook, Zukang Feng, et al.Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne posted to chapt_amino amino proteins by Diego_Prada on 2009-08-06 21:38:47 as along with 42 people and 5 groups viktor21614 badi ucbcjbm TLVincent maria_hauser Martin8223 tomjad flbarroso Taguan oceanwind dsmueller fisherp semin MarcoAlvarez kumar_physics LamBras RamuAnandakrishnan nlapalu reyez nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon aengisch debatebob massivemayhem gisle girschick selrac tji higueruelo boris_aguilar sebk timg References for 3DSim paper Radiation_Damage Stressosome biomedical-nlp beta
	Thermodynamic functions of conformational changes: conformational network of glycine diamide folding, entropy lowering, and informational accumulation. [My Copy] The journal of physical chemistry. A, Vol. 110, No. 49. (14 December 2006), pp. 13325-13331. by Szilard N. Fejer, Imre G. Csizmadia, Bela Viskolcz posted to amino cmn glycine by Diego_Prada on 2009-08-04 11:17:45 as
	Stereochemical Criteria for Polypeptide and Protein Chain ConformationsII. Allowed Conformations for a Pair of Peptide Units [My Copy] Biophysical Journal, Vol. 5, No. 6. (1 November 1965), pp. 909-933. by C. Ramakrishnan, G. N. Ramachandran posted to amino by Diego_Prada on 2009-07-29 17:20:12 as along with 2 people allmensch aqeel
	Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine ldquodipeptidesrdquo (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 50, No. 3. (15 February 2003), pp. 451-463. by Hao Hu, Marcus Elstner, Jan Hermans posted to amino dialanine force-fields by Diego_Prada on 2009-07-26 16:12:40 as along with 3 people flbarroso paddydu allmensch
	Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions [My Copy] Journal of Molecular Biology, Vol. 248, No. 2. (1995), pp. 361-373. by P. Maccallum, R. Poet, E. Jamesmilnerwhite posted to chapt_amino amino by Diego_Prada on 2009-07-20 17:35:08 as
	Coulombic attractions between partially chargedmain-chain atoms stabilise the right-handed twist found in most β-strands [My Copy] Journal of Molecular Biology, Vol. 248, No. 2. (1995), pp. 374-384. by P. Maccallum, R. Poet, E. Jamesmilnerwhite posted to amino by Diego_Prada on 2009-07-20 17:31:34 as
	The Folding Funnel Landscape of the Peptide Met-enkephalin [My Copy] (29 Oct 1998) by U. H. E. Hansmann, Y. Okamoto, J. Onuchic posted to enkaphalin by Diego_Prada on 2009-07-20 16:44:55 as
	The anatomy and taxonomy of protein structure. [My Copy] Advances in protein chemistry, Vol. 34 (1981), pp. 167-339. by J. S. Richardson posted to chapt_amino amino protein_folding proteins by Diego_Prada on 2009-07-18 18:21:51 as along with 1 person nikkiwithers

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chapter	60
ppi	44
dynamics	34
protein	32
allostery	30
dhfr	25
subdiffusion	24
water	22
energy_landscape	19
enzyme	18
folding	18
kinetics	17
review	17
free-energy	16
cap	15
simulation	15
binding	14
catalysis	13
protein-interactions	12
nmr	11
fractals	10
hierarchy	10
population_shifts	10
genome	9
hemoglobin	8
md	8
network	8
cap_dna	7
conformation	7
experimental	7
gpu	7
random_walk	7
dna	6
ligands	6
models	6
motion	5
mutations	5
transition	5
xray	5
algorithm	4
chemistry	4
clusterization	4
d4	4
docking	4
entropy	4
molecular_dynamics	4
myoglobin	4
shaw	4
tmd	4
acetyl	3
channel	3
dihedrals	3
networks	3
nma	3
normal_modes	3
relaxation_dispersion	3
structure	3
thermodynamics	3
vibrational_modes	3
alaninedipeptide	2
barrier	2
capri	2
complex	2
database	2
denatured	2
flory	2
kinases	2
landscape	2
mwc	2
side-chains	2
spectroscopy	2
state	2
temperature	2
tse	2
x-ray	2
alanine__scanning	1
analysis	1
asimmetry	1
b-factors	1
biology	1
book	1
charmm	1
clustering	1
community	1
comparison	1
computation	1
computational	1
cups	1
cyclophilin	1
ferrys_law	1
flexibility	1
gene_fusion	1
history	1
homology	1
homology_modelling	1
markov	1
master_equation	1
modularity	1
molecular	1
moore	1
other	1
pathways	1
pca	1
physical_chemistry	1
physics	1
pmf	1
prediction	1
profile	1
proteins	1
psichology	1
qmm	1
religion	1
remd	1
rmsd_restraints	1
rna	1
rubik	1
sampling	1
solvation	1
system-biology	1
target	1
wall	1

ruvido's watchlist [at least 200 articles] Export

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