ruvido's simulation [15 articles] Export

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

	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 simulation proteins clustering by ruvido on 2009-10-12 14:33:44 as along with 2 people allmensch Diego_Prada
	A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums [My Copy] The Journal of Chemical Physics, Vol. 120, No. 13. (2004), pp. 6085-6093. by Steven W. Rick posted to water simulation by ruvido on 2009-10-12 10:29:44 as along with 1 person Lombardo_7
	Absolute Free Energy and Entropy of a Mobile Loop of the Enzyme Acetylcholinesterase [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 22. (4 June 2009), pp. 7950-7964. by Mihail Mihailescu, Hagai Meirovitch posted to acetyl free-energy side-chains simulation by ruvido on 2009-07-02 09:26:37 as
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to gpu molecular_dynamics simulation by ruvido on 2009-02-18 10:05:41 as along with 10 people and 3 groups anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque sobolevnrm massivemayhem barry RamuAnandakrishnan baker-group structural_bioinformatics McCammon
	Molecular dynamics simulations of nucleic acid-protein complexes. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 194-199. by A. D. Mackerell, L. Nilsson posted to dna simulation by ruvido on 2008-03-14 15:37:59 as along with 4 people and 1 group flbarroso zwang sobolevnrm phoenixzxl baker-group
	Exploring reaction pathways with transition path and umbrella sampling: application to methyl maltoside. [My Copy] J Chem Phys, Vol. 124, No. 11. (21 March 2006) by R. J. Dimelow, R. A. Bryce, A. J. Masters, I. H. Hillier, N. A. Burton posted to free-energy simulation by ruvido on 2008-02-22 13:02:24 as along with 1 person bilab
	Investigating rare events by transition interface sampling [My Copy] Physica A: Statistical Mechanics and its Applications, Vol. 340, No. 1-3. (01 September 2004), pp. 395-401. by D. Moroni, T. Vanerp, P. Bolhuis posted to free-energy simulation by ruvido on 2008-02-22 13:00:39 as along with 2 people joshBerryman and_ped10
	A novel path sampling method for the calculation of rate constants [My Copy] J. Chem. Phys., Vol. 118 (May 2003), pp. 7762-7774. by T. S. van Erp, D. Moroni, P. G. Bolhuis posted to free-energy simulation by ruvido on 2008-02-22 12:57:29 as along with 1 person and_ped10
	Transition path sampling and the calculation of rate constants [My Copy] The Journal of Chemical Physics, Vol. 108, No. 5. (1998), pp. 1964-1977. by Christoph Dellago, Peter G. Bolhuis, Félix S. Csajka, David Chandler posted to free-energy simulation by ruvido on 2008-02-22 12:56:27 as along with 2 people jrperillaj tovrstra
	Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling [My Copy] Journal of Computational Physics, Vol. 23, No. 2. (February 1977), pp. 187-199. by G. Torrie, J. Valleau posted to free-energy pmf simulation by ruvido on 2008-02-22 12:54:40 as along with 2 people mc1975 sunnytov
	Hydride transfer catalysed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: coupled motions and distal mutations. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1472. (29 August 2006), pp. 1365-1373. by S. Hammes-Schiffer, J. B. Watney posted to binding catalysis chemistry dhfr enzyme kinetics ligands mutations qmm review simulation by ruvido on 2006-12-21 14:27:31 as
	Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6807-6812. by K. F. Wong, T. Selzer, S. J. Benkovic, S. Hammes-Schiffer posted to binding catalysis chemistry dhfr enzyme kinetics ligands md motion mutations simulation by ruvido on 2006-12-21 14:23:16 as
	Correlated motion and the effect of distal mutations in dihydrofolate reductase. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 12. (10 June 2003), pp. 6980-6985. by T. H. Rod, J. L. Radkiewicz, C. L. Brooks posted to binding catalysis chemistry dhfr enzyme ligands md motion mutations protein simulation by ruvido on 2006-12-21 14:20:49 as
	Phi-value analysis by molecular dynamics simulations of reversible folding. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 3. (18 January 2005), pp. 628-633. by G. Settanni, F. Rao, A. Caflisch posted to folding md simulation state transition tse by ruvido on 2006-12-19 14:19:12 as along with 2 people apaydin allmensch
	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 folding md network simulation state transition tse by ruvido on 2006-12-19 09:59:53 as along with 6 people and 1 group camster apaydin allmensch jlh64 nh Diego_Prada dbk-lab

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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 simulation [15 articles] Export

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