apaydin's Baker:D [20 articles] Export

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	Simultaneous prediction of protein folding and docking at high resolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18978-18983. by Rhiju Das, Ingemar AndrÃ©, Yang Shen, et al.Yibing Wu, Alexander Lemak, Sonal Bansal, Cheryl H. Arrowsmith, Thomas Szyperski, David Baker posted to protein_folding docking by apaydin on 2009-11-11 16:27:06 as along with 4 people ahmetbakan paulschlesinger ibuch zwang
	CASD-NMR: critical assessment of automated structure determination by NMR [My Copy] Nat Meth, Vol. 6, No. 9. (01 September 2009), pp. 625-626. by Antonio Rosato, Anurag Bagaria, David Baker, et al.Benjamin Bardiaux, Andrea Cavalli, Jurgen F. Doreleijers, Andrea Giachetti, Paul Guerry, Peter Guntert, Torsten Herrmann, Yuanpeng J. Huang, Hendrik R. A. Jonker, Binchen Mao, Therese E. Malliavin, Gaetano T. Montelione, Michael Nilges, Srivatsan Raman, Gijs van der Schot, Wim F. Vranken, Geerten W. Vuister, Alexandre M. J. J. Bonvin posted to nmr contacts by apaydin on 2009-09-13 13:58:00 as
	Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta [My Copy] Journal of Molecular Biology (08 July 2009) by Frank Dimaio, Michael D. Tyka, Matthew L. Baker, Wah Chiu, David Baker posted to electron_microscopy protein_structure_prediction by apaydin on 2009-08-07 06:13:45 as along with 2 people and 2 groups barry reyez structural_bioinformatics McCammon
	Sampling Bottlenecks in De novo Protein Structure Prediction. [My Copy] Journal of molecular biology (28 July 2009) by David E. Kim, Ben Blum, Philip Bradley, David Baker posted to protein_structure_prediction sampling by apaydin on 2009-07-30 11:32:51 as along with 3 people and 2 groups barry siggi84 reyez structural_bioinformatics McCammon
	De novo protein structure determination using sparse NMR data [My Copy] Journal of Biomolecular NMR, Vol. 18, No. 4. (1 December 2000), pp. 311-318. by Peter M. Bowers, Charlie E. M. Strauss, David Baker posted to nmr protein_structure_determination by apaydin on 2009-07-10 08:20:56 as
	Blind docking of pharmaceutically relevant compounds using RosettaLigand [My Copy] Protein Science, Vol. 18, No. 9. (24 June 2009), pp. 1998-2002. by Ian W. Davis, Kaushik Raha, Martha S. Head, David Baker posted to docking ligand-protein-binding by apaydin on 2009-07-04 08:48:01 as along with 1 person klexa
	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
	Kemp elimination catalysts by computational enzyme design [My Copy] Nature, Vol. 453, No. 7192. (19 March 2008), pp. 190-195. by Daniela Rothlisberger, Olga Khersonsky, Andrew M. Wollacott, et al.Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L. Gallaher, Eric A. Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N. Houk, Dan S. Tawfik, David Baker posted to enzyme_redesign by apaydin on 2009-02-26 09:53:52 as along with 12 people and 3 groups barmak7282 baiaixi whitead qbin1304 fralium Diego_Prada jwm msuarezdiez austin cactus neils sobolevnrm Jiang Research Group Biocatalysis and Biotransformation baker-group
	Prediction of membrane protein structures with complex topologies using limited constraints [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1409-1414. by P. Barth, B. Wallner, D. Baker posted to membrane protein_structure by apaydin on 2009-02-04 15:15:07 as along with 10 people and 2 groups rph dgront sebk barry krapnik viktor21614 paulschlesinger zwang agrossfield amishp OPIG structural_bioinformatics
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to design protein by apaydin on 2009-01-25 16:32:39 as along with 10 people bmduggan kgutwin Diego_Prada onufriev dfgreen jwm hmk heymiki kevinchannon ca3295
	Consistent blind protein structure generation from NMR chemical shift data [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4685-4690. by Yang Shen, Oliver Lange, Frank Delaglio, et al.Paolo Rossi, James M. Aramini, Gaohua Liu, Alexander Eletsky, Yibing Wu, Kiran K. Singarapu, Alexander Lemak, Alexandr Ignatchenko, Cheryl H. Arrowsmith, Thomas Szyperski, Gaetano T. Montelione, David Baker, Ad Bax posted to chemical nmr prediction protein shifts structure by apaydin on 2008-07-05 20:30:20 as along with 7 people and 1 group siggi84 babakap dgront zwang biehl sunhwan skoddet Nielsen group
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted to molecular prediction protein replacement structure by apaydin on 2008-02-18 00:04:34 as along with 16 people and 2 groups bmduggan newton1234 aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway ardalby baker-group OPIG
	De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. [My Copy] J Am Chem Soc, Vol. 124, No. 11. (20 March 2002), pp. 2723-2729. by C. A. Rohl, D. Baker posted to denovo determination protein rdc rosetta structure by apaydin on 2007-10-30 18:02:03 as along with 1 person j3xucite
	Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein−Protein Interface [My Copy] Journal of Molecular Biology, Vol. 361,, No. 1. (August 2006), pp. 195-208. by Lukasz A. Joachimiak, Tanja Kortemme, Barry, David Baker posted to protein_design protein_protein_binding by apaydin on 2006-09-06 16:49:18 as
	A ?solvated rotamer? approach to modeling water-mediated hydrogen bonds at protein-protein interfaces [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 4. (2005), pp. 893-904. by Lin Jiang, Brian Kuhlman, Tanja Kortemme, David Baker posted to hydrogen_bonds protein_protein_binding rotamer side_chain_flexibility solvation solvent_effects by apaydin on 2006-06-16 15:01:40 as along with 4 people oceanwind jwm skoddet msuarezdiez
	Computational redesign of endonuclease DNA binding and cleavage specificity [My Copy] Nature, Vol. 441, No. 7093. (1 June 2006), pp. 656-659. by Justin Ashworth, James J. Havranek, Carlos M. Duarte, et al.Django Sussman, Raymond J. Monnat, Barry L. Stoddard, David Baker posted to enzyme_redesign monte_carlo protein_design protein_dna_binding by apaydin on 2006-06-05 16:18:23 as along with 4 people and 1 group dfgreen aalibes jwm condon beta
	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
	Rapid protein fold determination using unassigned NMR data. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 26. (23 December 2003), pp. 15404-15409. by J. Meiler, D. Baker posted to fold_determination nmr unassigned_nmr_data by apaydin on 2005-08-10 14:14:47 as along with 2 people babakap j3xucite
	Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (4 September 2003), pp. 262-272. by William J. Wedemeyer, David Baker posted to efficient_energy_minimization by apaydin on 2005-05-17 23:03:16 as along with 1 person gane5h
	Exploring folding free energy landscapes using computational protein design [My Copy] Current Opinion in Structural Biology, Vol. 14, No. 1. (February 2004), pp. 89-95. by Brian Kuhlman, David Baker posted to protein_design review by apaydin on 2005-05-12 18:55:59 as

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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
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equation	1
electron_microscopy	1
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long	1
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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

apaydin's Baker:D [20 articles] Export

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