CiteULike: apaydin's rate_determination [14 articles]

Common Motifs and Topological Effects in the Protein Folding Transition State

Journal of Molecular Biology, Vol. 359, No. 4. (16 June 2006), pp. 1075-1085.

by Isaac A. Hubner, Magnus Lindberg, Ellinor Haglund, Mikael Oliveberg, Eugene I. Shakhnovich

posted to folding molecular_dynamics pfold phi_value_analysis protein_dynamics protein_folding rate_determination rate_prediction transition_state_ensemble by apaydin on 2006-06-11 16:28:27 as

Folding nuclei in proteins.

FEBS Lett, Vol. 489, No. 2-3. (2 February 2001), pp. 113-118.

by O. V. Galzitskaya, D. N. Ivankov, A. V. Finkelstein

posted to go_model phi_value_analysis protein_folding rate_determination rate_prediction by apaydin on 2006-05-13 14:33:44 as

TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark - Annual Review of Physical Chemistry, 53(1):291 - Abstract

by Dellago, Bolhuis

posted to rate_determination review by apaydin on 2006-04-12 13:32:13 as

transition path sampling

by Dellago, Bolhuis

posted to rate_determination by apaydin on 2006-04-12 13:31:12 as

Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein.

Biochemistry, Vol. 34, No. 21. (30 May 1995), pp. 7217-7224.

by B. B. Kragelund, C. V. Robinson, J. Knudsen, C. M. Dobson, F. M. Poulsen

posted to acbp rate_determination by apaydin on 2006-04-12 11:29:17 as

Reaction coordinates and rates from transition paths.

Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6732-6737.

by Robert B. Best, Gerhard Hummer

posted to pfold protein_folding rate_determination by apaydin on 2006-02-16 20:16:40 as read

along with 4 people allmensch bilab mtw jlh64

Folding Thermodynamics of Model Four-Strand Antiparallel beta -Sheet Proteins

Biophys. J., Vol. 82, No. 2. (1 February 2002), pp. 646-659.

by Hyunbum Jang, Carol K. Hall, Yaoqi Zhou

posted to protein_folding rate_determination by apaydin on 2006-02-09 16:03:45 as

Folding Rate Prediction Using Total Contact Distance

Biophys. J., Vol. 82, No. 1. (1 January 2002), pp. 458-463.

by Hongyi Zhou, Yaoqi Zhou

posted to protein_folding rate_determination by apaydin on 2006-02-09 16:02:23 as read

Characterizing transition states in protein folding: an essential step in the puzzle

Current Opinion in Structural Biology, Vol. 5, No. 1. (February 1995), pp. 79-84.

by Alan R. Fersht

posted to phi_value_analysis protein_folding rate_determination review by apaydin on 2006-01-07 13:32:02 as

Theoretical study of protein folding: outlining folding nuclei and estimation of protein folding rates

Journal of Physics: Condensed Matter, Vol. 17, No. 18. (2005), pp. S1539-S1551.

by O. V. Galzitskaya, S. O. Garbuzynskiy, A. V. Finkelstein

posted to phi_value_analysis protein_folding rate_determination by apaydin on 2006-01-03 17:27:41 as read

Theoretical Study of a Landscape of Protein Folding-Unfolding Pathways. Folding Rates at Midtransition

posted to protein_folding rate_determination by apaydin on 2005-12-20 21:28:28 as read

cm5_18_011.pdf (application/pdf Object)

posted to phi_value_analysis protein_folding rate_determination by apaydin on 2005-12-20 17:55:50 as

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.

Proc Natl Acad Sci U S A, Vol. 96, No. 20. (28 September 1999), pp. 11305-11310.

by E. Alm, D. Baker

posted to phi_value_analysis protein_folding rate_determination by apaydin on 2005-12-13 21:38:38 as read

Outlining folding nuclei in globular proteins.

J Mol Biol, Vol. 336, No. 2. (13 February 2004), pp. 509-525.

by S. O. Garbuzynskiy, A. V. Finkelstein, O. V. Galzitskaya

posted to go_model phi_value_analysis protein_folding rate_determination by apaydin on 2005-12-12 21:53:55 as read

along with 1 person choonpeng

	Common Motifs and Topological Effects in the Protein Folding Transition State [My Copy] Journal of Molecular Biology, Vol. 359, No. 4. (16 June 2006), pp. 1075-1085. by Isaac A. Hubner, Magnus Lindberg, Ellinor Haglund, Mikael Oliveberg, Eugene I. Shakhnovich posted to folding molecular_dynamics pfold phi_value_analysis protein_dynamics protein_folding rate_determination rate_prediction transition_state_ensemble by apaydin on 2006-06-11 16:28:27 as
	Folding nuclei in proteins. [My Copy] FEBS Lett, Vol. 489, No. 2-3. (2 February 2001), pp. 113-118. by O. V. Galzitskaya, D. N. Ivankov, A. V. Finkelstein posted to go_model phi_value_analysis protein_folding rate_determination rate_prediction by apaydin on 2006-05-13 14:33:44 as
	TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark - Annual Review of Physical Chemistry, 53(1):291 - Abstract [My Copy] by Dellago, Bolhuis posted to rate_determination review by apaydin on 2006-04-12 13:32:13 as
	transition path sampling [My Copy] by Dellago, Bolhuis posted to rate_determination by apaydin on 2006-04-12 13:31:12 as
	Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein. [My Copy] Biochemistry, Vol. 34, No. 21. (30 May 1995), pp. 7217-7224. by B. B. Kragelund, C. V. Robinson, J. Knudsen, C. M. Dobson, F. M. Poulsen posted to acbp rate_determination by apaydin on 2006-04-12 11:29:17 as
	Reaction coordinates and rates from transition paths. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6732-6737. by Robert B. Best, Gerhard Hummer posted to pfold protein_folding rate_determination by apaydin on 2006-02-16 20:16:40 as along with 4 people allmensch bilab mtw jlh64
	Folding Thermodynamics of Model Four-Strand Antiparallel beta -Sheet Proteins [My Copy] Biophys. J., Vol. 82, No. 2. (1 February 2002), pp. 646-659. by Hyunbum Jang, Carol K. Hall, Yaoqi Zhou posted to protein_folding rate_determination by apaydin on 2006-02-09 16:03:45 as
	Folding Rate Prediction Using Total Contact Distance [My Copy] Biophys. J., Vol. 82, No. 1. (1 January 2002), pp. 458-463. by Hongyi Zhou, Yaoqi Zhou posted to protein_folding rate_determination by apaydin on 2006-02-09 16:02:23 as
	Characterizing transition states in protein folding: an essential step in the puzzle [My Copy] Current Opinion in Structural Biology, Vol. 5, No. 1. (February 1995), pp. 79-84. by Alan R. Fersht posted to phi_value_analysis protein_folding rate_determination review by apaydin on 2006-01-07 13:32:02 as
	Theoretical study of protein folding: outlining folding nuclei and estimation of protein folding rates [My Copy] Journal of Physics: Condensed Matter, Vol. 17, No. 18. (2005), pp. S1539-S1551. by O. V. Galzitskaya, S. O. Garbuzynskiy, A. V. Finkelstein posted to phi_value_analysis protein_folding rate_determination by apaydin on 2006-01-03 17:27:41 as
	Theoretical Study of a Landscape of Protein Folding-Unfolding Pathways. Folding Rates at Midtransition [My Copy] posted to protein_folding rate_determination by apaydin on 2005-12-20 21:28:28 as
	cm5_18_011.pdf (application/pdf Object) [My Copy] posted to phi_value_analysis protein_folding rate_determination by apaydin on 2005-12-20 17:55:50 as
	Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. [My Copy] Proc Natl Acad Sci U S A, Vol. 96, No. 20. (28 September 1999), pp. 11305-11310. by E. Alm, D. Baker posted to phi_value_analysis protein_folding rate_determination by apaydin on 2005-12-13 21:38:38 as
	Outlining folding nuclei in globular proteins. [My Copy] J Mol Biol, Vol. 336, No. 2. (13 February 2004), pp. 509-525. by S. O. Garbuzynskiy, A. V. Finkelstein, O. V. Galzitskaya posted to go_model phi_value_analysis protein_folding rate_determination by apaydin on 2005-12-12 21:53:55 as along with 1 person choonpeng

apaydin's rate_determination [14 articles] Export

apaydin's tags

nmr	188
protein	108
protein_dynamics	106
protein_folding	66
review	52
folding	51
protein_structure_determination	43
structure	39
assignments	39
protein_ligand_binding	34
protein_design	26
rdc	26
prediction	19
tutorial	18
protein_protein_binding	18
resonance_assignment	18
dynamics	16
normal_mode_analysis	15
rate_determination	14
chemical	14
allostery	14
unfolded_state	14
phi_value_analysis	13
backbone	13
determination	13
prm	13
pfold	12
model	12
noe	11
ligand-protein-binding	11
nma	11
rate	10
misfolding	10
shift	10
x-ray	9
flexibility	9
noe_assignment	9
sba	9
protein_structure	9
molecular_dynamics	9
sampling	8
motion	8
docking	8
voting	8
design	8
database	7
rotamer_libraries	7
molecular	7
homology	7
probabilistic_roadmaps	7
function	7
rate_prediction	7
algorithms	6
alignment	6
planning	6
go_model	6
rotamer	6
protein_protein_interactions	6
srs	6
ensemble	6
unassigned_nmr_data	6
conformational	6
chemical_shift	5
scoring	5
structural	5
markov_chains	5
side_chain_flexibility	5
relaxation	5
resonance	5
enm	5
ensembles	5
based	5
monte_carlo	5
binding	5
nvr	5
sidechain	5
programming	5
hiv_integrase	4
webserver	4
analysis	4
inverse_kinematics	4
coarse_grained	4
shifts	4
denatured	4
network	4
kinetics	4
learning	4
4d-noesy	4
ligand_flexibility	4
hydrogen_exchange	4
entropy	4
drug	4
aggregation	3
teaching	3
integer	3
fast	3
intermediate	3
pathways	3
parameter	3
loop	3
order	3
diffusion	3
enzyme_redesign	3
python	3
simulations	3
fold_determination	3
gnm	3
transition_state_ensemble	3
linear	3
energy	3
denatured_state	3
rigidity	3
protein_structure_prediction	3
collision	3
elastic	3
molecular_replacement	3
torsional_angle	3
saxs	3
backbone_flexibility	3
search	3
consensus	3
fragment	2
secondary	2
simulated	2
mfpt	2
finkelstein	2
reference	2
detection	2
noise_stability	2
methods	2
cap	2
lattice	2
markov_random_field	2
solvent_effects	2
optimization	2
phi	2
colony	2
unfolded	2
kinematics	2
landscape	2
inverse	2
modelling	2
efficient_energy_minimization	2
ligand	2
negative_design	2
hydrogen_bonds	2
molecular_mechanics	2
hp	2
kstar	2
comparison	2
path	2
xray	2
diversity	2
replacement	2
metadynamics	2
tool	2
milestoning	2
fold	2
funnel	2
space	2
gpcr	2
nrps	2
acbp	2
energy_landscape	2
cheminformatics	2
ant	2
couplings	2
transition	2
value	2
visualization	2
data	2
contacts	2
annealing	2
incremental	2
recognition	2
solvation	2
hotspot	2
modeling	2
genetic	2
index	2
systems_biology	2
mass_spectrometry	2
corex	2
native	2
closure	2
equilibrium	2
approximation	2
bipartite_matching	2
energy_function	1
comparing_different_motion_models	1
equation	1
electron_microscopy	1
paramagnetic_quenching	1
long	1
modeller	1
pca	1
lambda	1
molecular_design	1
distance_measure	1
supercomputer	1
entropy_estimation	1
kinetic	1
bpti	1
classification	1
ddg	1
sequential	1
supramolecular	1
propagation	1
essential_dynamics	1
protein_stability	1
ruby	1
disordered_proteins	1
example	1
em	1
umbrella_sampling	1
membrane	1
software	1
inverse_folding	1
plot	1
svm	1
opinion	1
function_prediction	1
structural_ensemble	1
manipulation_planning	1
anm	1
communication	1
evolution	1
electrostatics	1
study	1
information	1
constraint_satisfaction	1
tensor	1
geometry	1
maps	1
homologous	1
thermodynamics	1
foldamer	1
completeness	1
empirical_scoring_function	1
principal	1
cyana	1
cloud_computing	1
flexibiliy	1
advice	1
mr	1
benchmark	1
c-alpha	1
calculation	1
finding	1
exchange	1
multiscale	1
empirical	1
time	1
free	1
metaheuristics	1
robotics	1
residue	1
anisotropic	1
multidomain	1
peptides	1
cryo	1
experimental	1
tabu	1
rna	1
averaging	1
branch_and_bound	1
graph_theory	1
protein_dna_binding	1
refinement	1
macromolecular	1
functional_classification	1
froda	1
hardware	1
content	1
initiative	1
master	1
sh3	1
topology	1
linguistics	1
constant	1
pre	1
mars	1
local	1
folder	1
screening	1
disordered	1
wide-angle	1
assembly	1
opensource	1
thermodynamic	1
scattering	1
library	1
psi-value-analysis	1
sequence	1
optimum	1
motif	1
wavelets	1
graph_representation	1
kariyer	1
croem	1
pattern	1
perspectives	1
ubiquitin	1
foldtraj	1
water_hsqc	1
score	1
mirna	1
fft	1
belief	1
dimensionality_reduction	1
denovo	1
replica	1
experiments	1
bayesian_methods	1
cdc25	1
d-amino-acid	1
ribosome	1
rosetta	1
geometric	1
tools	1
multipole	1
binding_site	1
repressor	1
state	1
go	1
non-holonomic	1
difference_map	1
organization	1
stochasticity	1
component	1
charges	1
complete	1
mle	1
simplified	1
comment	1
mining	1
elnemo	1
configurational	1
synthesis	1
atomic	1
partial	1
hd_exchange_rate	1
meta	1
dipolar	1
drug_discovery	1
density	1
redcat	1
placement	1
chevron	1
scoring_function	1
ligand_binding	1
pnas	1
hausdorff	1
drug_design	1
complex	1
task_planning	1
crystallography	1
kl_distance	1
waiting_time	1
germany	1
graph_cuts	1
research	1
refolding	1
conformational_sampling	1
md	1