apaydin's library 637 articles Export

Ordered by to_read.

	Automated analysis of NMR assignments and structures for proteins [My Copy] Current Opinion in Structural Biology, Vol. 9, No. 5. (1 October 1999), pp. 635-642. by Hunter N. B. Moseley, Gaetano T. Montelione posted to assignments determination nmr protein review structure by apaydin on 2007-09-07 16:31:57 as along with 1 person kumar_physics
	Automated Protein Structure Determination from NMR Spectra [My Copy] J. Am. Chem. Soc. (2006) by Blanca López-Méndez, Peter Güntert posted to nmr protein_structure_determination by apaydin on 2006-09-21 14:40:54 as
	Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin. [My Copy] Proteins, Vol. 46, No. 2. (1 February 2002), pp. 215-224. by H. Schäfer, L. J. Smith, A. E. Mark, W. F. van Gunsteren posted to entropy protein_design rotamer by apaydin on 2006-03-09 18:47:59 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
	HOT_NC05_fast_deep_nets.pdf (application/pdf Object) [My Copy] by Osindero posted to learning by apaydin on 2005-12-12 04:59:58 as
	advice to postdocs [My Copy] posted to no-tag by apaydin on 2005-12-05 18:19:33 as
	Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization -- Lindahl and Delarue 33 (14): 4496 -- Nucleic Acids Research [My Copy] posted to protein_dynamics protein_ligand_binding side_chain_flexibility by apaydin on 2005-09-08 13:28:40 as
	rotamer pair energy calculations using a trie data structure [My Copy] by Leaver-Fay, Kuhlman, Snoeyink posted to protein_design rotamer_libraries by apaydin on 2005-08-04 20:19:32 as
	The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy [My Copy] Journal of Magnetic Resonance, Vol. 173, No. 2. (April 2005), pp. 310-316. by Jens Meiler, David Baker posted to nmr sba assignments by apaydin on 2009-04-27 16:17:37 as along with 1 person karbak
	Automated structure determination from NMR spectra [My Copy] European Biophysics Journal, Vol. 38, No. 2. (1 February 2009), pp. 129-143. by Peter Güntert posted to nmr review by apaydin on 2009-03-31 13:36:52 as along with 3 people dgront lna bmduggan
	Molecular dynamics and protein function. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6679-6685. by M. Karplus, J. Kuriyan posted to molecular_dynamics review by apaydin on 2007-06-05 14:46:38 as along with 5 people flbarroso onufriev bilab allmensch RamuAnandakrishnan
	NMR studies of protein structure and dynamics [My Copy] Journal of Magnetic Resonance, Vol. 173, No. 2. (April 2005), pp. 193-207. by Lewis E. Kay posted to dynamics nmr protein review structure by apaydin on 2007-06-05 14:40:28 as
	Residual dipolar couplings: synergy between NMR and structural genomics. [My Copy] J Biomol NMR, Vol. 22, No. 1. (January 2002), pp. 1-8. by H. M. Al-Hashimi, D. J. Patel posted to cap nmr nvr sba by apaydin on 2007-04-24 15:12:07 as
	Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. [My Copy] J Mol Biol, Vol. 318, No. 3. (3 May 2002), pp. 637-649. by H. M. Al-Hashimi, A. Gorin, A. Majumdar, Y. Gosser, D. J. Patel posted to cap nmr nvr sba by apaydin on 2007-04-24 15:08:47 as
	Folding rates and low-entropy-loss routes of two-state proteins. [My Copy] J Mol Biol, Vol. 329, No. 3. (6 June 2003), pp. 585-598. by T. R. Weikl, K. A. Dill posted to srs rate protein prediction folding entropy by apaydin on 2007-01-19 21:39:58 as
	Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation [My Copy] Proteins: Structure, Function, and Genetics, Vol. 20, No. 1. (1994), pp. 68-84. by Kon H. Lee, Dong Xie, Ernesto Freire, Mario L. Amzel posted to study sidechain folding entropy empirical configurational binding by apaydin on 2007-01-17 22:31:42 as along with 1 person gisle
	The magnitude of the backbone conformational entropy change in protein folding. [My Copy] Proteins, Vol. 25, No. 2. (June 1996), pp. 143-156. by J. A. D'Aquino, J. Gómez, V. J. Hilser, K. H. Lee, L. M. Amzel, E. Freire posted to protein folding entropy conformational backbone by apaydin on 2007-01-17 22:29:56 as along with 1 person rsantana
	Model-based assignment and inference of protein backbone Nuclear Magnetic Resonances. [My Copy] Statistical applications in genetics and molecular biology, Vol. 3, No. 1. (2004) by Olga Vitek, Jan Vitek, Bruce Craig, Chris Bailey-Kellogg posted to chemical function nmr resonance scoring shift assignments by apaydin on 2006-11-27 15:00:16 as along with 1 person babakap
	Error analysis and efficient sampling in Markovian state models for molecular dynamics. [My Copy] J Chem Phys, Vol. 123, No. 20. (22 November 2005) by N. Singhal, V. S. Pande posted to markov_chains mfpt molecular_dynamics pfold prm probabilistic_roadmaps by apaydin on 2006-05-25 01:36:37 as along with 1 person dimka
	combining voters [My Copy] by Alpaydin posted to bipartite_matching learning nmr nvr resonance_assignment voting by apaydin on 2006-05-24 23:46:50 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 aggregation folding markov_chains pfold prm probabilistic_roadmaps protein_folding by apaydin on 2006-05-21 19:59:06 as along with 2 people Diego_Prada mtw
	The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. [My Copy] Proc Natl Acad Sci U S A, Vol. 95, No. 17. (18 August 1998), pp. 9903-9908. by V. J. Hilser, D. Dowdy, T. G. Oas, E. Freire posted to allostery folding protein by apaydin on 2006-05-09 22:27:03 as along with 4 people lna aqeel shuns choonpeng
	Approximation algorithms for classification problems with pairwise relationships: metric labeling and Markov random fields [My Copy] J. ACM, Vol. 49, No. 5. (September 2002), pp. 616-639. by Jon Kleinberg, \ &\#201;va Tardos posted to markov_random_field nvr resonance_assignment by apaydin on 2006-04-27 17:12:08 as along with 1 person ansobol
	Histogram-based scoring schemes for protein NMR resonance assignment. [My Copy] J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 747-764. by X. Wan, T. Tegos, G. Lin posted to nmr resonance_assignment scoring by apaydin on 2006-03-28 21:16:28 as
	Interhelical angle and distance preferences in globular proteins. [My Copy] Biophys J, Vol. 86, No. 2. (February 2004), pp. 1105-1117. by S. Lee, G. S. Chirikjian posted to protein_design rotamer by apaydin on 2006-03-27 17:01:43 as
	Reconsidering complete search algorithms for protein backbone NMR assignment. [My Copy] Bioinformatics, Vol. 21 Suppl 2 (1 September 2005) by O. Vitek, C. Bailey-Kellogg, B. Craig, P. Kuliniewicz, J. Vitek posted to nmr resonance_assignment by apaydin on 2006-03-22 23:06:02 as along with 1 person j3xucite
	High-Resolution Protein Design with Backbone Freedom [My Copy] Science, Vol. 282, No. 5393. (20 November 1998), pp. 1462-1467. by Pehr B. Harbury, Joseph J. Plecs, Bruce Tidor, Tom Alber, Peter S. Kim posted to backbone_flexibility protein_design protein_dynamics by apaydin on 2006-03-15 23:35:59 as along with 2 people kgutwin dfgreen
	Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO) [My Copy] Journal of Biomolecular NMR, Vol. 32, No. 3. (July 2005), pp. 219-233. by Hamid Eghbalnia, Arash Bahrami, Liya Wang, Amir Assadi, John Markley posted to nmr protein_structure by apaydin on 2006-03-13 15:28:56 as along with 1 person rph
	Flexible ligand docking using conformational ensembles. [My Copy] Protein Sci, Vol. 7, No. 4. (April 1998), pp. 938-950. by D. M. Lorber, B. K. Shoichet posted to binding ensembles ligand-protein-binding rotamer by apaydin on 2006-03-09 20:25:26 as
	Evaluating the quality of NMR structures by local density of protons. [My Copy] Proteins, Vol. 62, No. 4. (1 March 2006), pp. 852-864. by Y. E. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner posted to nmr protein_structure by apaydin on 2006-03-08 23:42:16 as
	Reassessing random-coil statistics in unfolded proteins [My Copy] PNAS, Vol. 101, No. 34. (24 August 2004), pp. 12497-12502. by Nicholas C. Fitzkee, George D. Rose posted to misfolding protein_folding unfolded_state by apaydin on 2006-02-16 19:22:30 as along with 3 people thamelry allmensch rph
	NMR studies of protein interactions [My Copy] by Koh Takeuchi, Gerhard Wagner posted to nmr protein_protein_binding review by apaydin on 2006-02-14 20:18:12 as
	Protein structure elucidation from NMR proton densities [My Copy] PNAS, Vol. 99, No. 10. (14 May 2002), pp. 6713-6718. by Alexander Grishaev, M. Llinás posted to nmr noe_assignment protein_structure_determination resonance_assignment by apaydin on 2006-02-13 14:51:52 as
	CLOUDS, a protocol for deriving a molecular proton density via NMR [My Copy] PNAS, Vol. 99, No. 10. (14 May 2002), pp. 6707-6712. by Alexander Grishaev, M. Llinás posted to molecular_replacement nmr noe noe_assignment protein_structure_determination rdc resonance_assignment unassigned_nmr_data by apaydin on 2006-02-13 14:49:21 as along with 1 person rph
	Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. [My Copy] Angewandte Chemie (International ed. in English), Vol. 42, No. 24. (23 June 2003), pp. 2718-2736. by Andrew M. Davis, Simon J. Teague, Gerard J. Kleywegt posted to ligand_flexibility protein_dynamics protein_ligand_binding by apaydin on 2006-02-10 15:49:51 as along with 3 people and 2 groups oteri sangeetha thanatos Bioinformatics insilicodrug
	Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy [My Copy] posted to ligand_flexibility protein_dynamics protein_ligand_binding by apaydin on 2006-02-10 15:46:38 as
	Benjamini, Kalai, Schramm: Noise sensitivity of boolean functions and applications to percolation [My Copy] posted to noise_stability voting by apaydin on 2006-02-03 23:45:38 as
	Real time inverse kinematics for general 6R manipulators [My Copy] Robotics and Automation, 1992. Proceedings., 1992 IEEE International Conference on (1992), pp. 383-389 vol.1. by D. Manocha, J. F. Canny posted to inverse_kinematics by apaydin on 2006-01-25 20:17:50 as along with 1 person and 1 group jimesh Inverse_Kinematics
	efficient IK for general 6R manipulators [My Copy] by Manocha, Canny posted to inverse_kinematics by apaydin on 2006-01-25 20:16:00 as
	Efficient generation of feasible pathways for protein conformational transitions. [My Copy] Biophys J, Vol. 83, No. 3. (September 2002), pp. 1620-1630. by M. K. Kim, R. L. Jernigan, G. S. Chirikjian posted to coarse_grained normal_mode_analysis protein_dynamics by apaydin on 2006-01-17 00:25:35 as along with 1 person aqeel
	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
	protein unfolding with first [My Copy] by Thorpe, Hespenheide posted to phi_value_analysis protein_dynamics protein_folding by apaydin on 2006-01-03 20:56:51 as
	bayesian methods for machine learning [My Copy] by Neal posted to bayesian_methods tutorial by apaydin on 2006-01-02 18:07:05 as
	The family feud: do proteins with similar structures fold via the same pathway? [My Copy] Curr Opin Struct Biol, Vol. 15, No. 1. (February 2005), pp. 42-49. by A. Zarrine-Afsar, S. M. Larson, A. R. Davidson posted to phi_value_analysis protein_folding review by apaydin on 2005-12-22 19:29:43 as along with 1 person gbart
	Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. [My Copy] Proc Natl Acad Sci U S A (14 December 2005) by Dror Tobi, Ivet Bahar posted to normal_mode_analysis protein_dynamics protein_ligand_binding protein_protein_binding by apaydin on 2005-12-18 17:04:10 as along with 3 people aqeel shuns insectopalo
	Describing Partially Unfolded States of Proteins from Sparse NMR Ddata [My Copy] Journal of Biomolecular NMR, Vol. 33, No. 3. (November 2005), pp. 175-186. by Gloria Fuentes, Aart Nederveen, Robert Kaptein, Rolf Boelens, Alexandre Bonvin posted to nmr protein_folding by apaydin on 2005-12-16 05:06:36 as along with 1 person gloria
	Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model. [My Copy] J Chem Phys, Vol. 120, No. 14. (8 April 2004), pp. 6769-6778. by P. Lenz, B. Zagrovic, J. Shapiro, V. S. Pande posted to pfold by apaydin on 2005-12-12 16:02:00 as
	Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 55, No. 3. (5 March 2004), pp. 635-645. by Cristian Micheletti, Paolo Carloni, Amos Maritan posted to comparing_different_motion_models protein_dynamics by apaydin on 2005-12-08 15:49:35 as along with 1 person aqeel
	Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. [My Copy] Proteins, Vol. 51, No. 1. (1 April 2003), pp. 41-55. by M. A. DePristo, P. I. de Bakker, S. C. Lovell, T. L. Blundell posted to protein_dynamics protein_structure_determination by apaydin on 2005-11-18 18:47:42 as
	wafr.pdf (application/pdf Object) [My Copy] by Lotan, Latombe posted to protein_dynamics by apaydin on 2005-11-16 21:41:13 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics

Note: You may cite this page as: http://www.citeulike.org/user/apaydin/order/to_read

Result page: 1 2 3 4 5 6 7 8 9 10 Next

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

apaydin's library 637 articles Export

apaydin's tags