apaydin's protein [108 articles] Export

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	How to mark off paths on the protein energy landscape [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18879-18880. by Martin Gruebele posted to protein folding energy_landscape by apaydin on 2009-11-11 16:26:43 as
	Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 19011-19016. by Frank NoÃ©, Christof SchÃ¼tte, Eric Vanden-Eijnden, Lothar Reich, Thomas R. Weikl posted to protein folding by apaydin on 2009-11-11 16:18:08 as along with 1 person Diego_Prada
	Nature of the protein universe [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 27. (7 July 2009), pp. 11079-11084. by Michael Levitt posted to protein review by apaydin on 2009-07-04 08:45:08 as along with 9 people and 1 group martainn pmung ldiambra VGreiff carlosjavierna philcarter TRHvidsten paulschlesinger renatomilani Orengo Group Journal Picks
	The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation [My Copy] Genome Biology, Vol. 9 (16 January 2008), R8. by Shirley Wu, Mike P. Liang, Russ B. Altman posted to determination function protein by apaydin on 2009-05-22 06:44:24 as along with 1 person kiekyon
	Structural biology. Dynamic visions of enzymatic reactions. [My Copy] Science, Vol. 313, No. 5793. (15 September 2006), pp. 1586-1587. by M. Vendruscolo, C. M. Dobson posted to folding perspectives protein stochasticity by apaydin on 2009-05-20 07:13:25 as along with 2 people victorclaessen tny
	Shmygelska_Alena.pdf (application/pdf Object) [My Copy] by Shmygelska posted to ant colony folding optimization protein by apaydin on 2009-05-20 05:49:13 as
	Structural Interpretation of Paramagnetic Relaxation Enhancement-Derived Distances for Disordered Protein States [My Copy] Journal of Molecular Biology, Vol. 390, No. 3. (17 July 2009), pp. 467-477. by Debabani Ganguly, Jianhan Chen posted to denatured ensemble folding nmr pre protein by apaydin on 2009-05-19 09:59:22 as
	The folding mechanism of BBL: Plasticity of transition state structure observed within an ultrafast folding protein family [My Copy] by Hannes Neuweilera, Timothy, Trevor J. Rutherforda, et al.Christopher M. Johnsona, Mark D. Allena, Neil, Alan R. Fersht posted to folding protein transition_state_ensemble by apaydin on 2009-05-14 06:37:56 as
	Different members of a simple 3-helix bundle protein family have very different folding rates and fold by different mechanisms [My Copy] by Beth G. Wensleya, Martina Gärtner[1], Wan X. Chooa, Sarah Batey2, And posted to folding protein rate by apaydin on 2009-05-14 06:35:10 as
	Nothing about protein structure classification makes sense except in the light of evolution [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (24 June 2009), pp. 329-334. by Ruben E. Valas, Song Yang, Philip E. Bourne posted to classification evolution protein structure by apaydin on 2009-05-12 08:50:42 as along with 13 people and 3 groups dfdong mkotlyar skywalkerus02 dgront nyyu robfsouza barry coela Zephyrus sobolevnrm zwang friendpine paulschlesinger structural_bioinformatics R.E.A.D baker-group
	msmbuilder [My Copy] by Pande posted to folding kinetics protein srs by apaydin on 2009-05-10 17:59:36 as
	Finding the Consensus Shape for a Protein Family [My Copy] Algorithmica, Vol. 38, No. 1. (1 October 2003), pp. 115-129. by Paul L. Chew, Klara Kedem posted to consensus protein structure by apaydin on 2009-05-10 17:52:16 as
	Parameter optimization for the Gaussian model of protein folding [My Copy] Polymer, Vol. 43, No. 2. (January 2002), pp. 495-501. by A. Erkip posted to folding protein by apaydin on 2009-05-06 17:12:11 as
	Fast procedure for reconstruction of full-atom protein models from reduced representations. [My Copy] Journal of computational chemistry, Vol. 29, No. 9. (15 July 2008), pp. 1460-1465. by Piotr Rotkiewicz, Jeffrey Skolnick posted to consensus protein structure by apaydin on 2009-04-26 14:57:43 as along with 5 people Gabriel439 sebk rsantana mijam middledomain
	improving consensus structure [My Copy] by Dukka posted to consensus protein structure by apaydin on 2009-04-26 14:53:36 as
	Topological methods for exploring low-density states in biomolecular folding pathways. [My Copy] by Pande, Guibas posted to folding pathways protein topology by apaydin on 2009-04-26 10:06:28 as
	Similarity Measures for Protein Ensembles [My Copy] PLoS ONE, Vol. 4, No. 1. (15 January 2009), e4203. by Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg posted to comparison ensembles protein by apaydin on 2009-04-12 07:59:36 as along with 8 people and 3 groups anuragsethi klexa sobolevnrm gane5h barry jmccammon reyez biehl baker-group structural_bioinformatics McCammon
	Relaxation Dispersion NMR Spectroscopy as a Tool for Detailed Studies of Protein Folding [My Copy] Vol. 96, No. 6. (18 March 2009), pp. 2045-2054. by Philipp Neudecker, Patrik Lundström, Lewis E. Kay posted to folding nmr protein by apaydin on 2009-03-20 10:02:36 as
	Protein segment finder: an online search engine for segment motifs in the PDB. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (January 2009) by A. O. Samson, M. Levitt posted to motif protein by apaydin on 2009-03-08 11:16:27 as
	Rapid Sampling of Molecular Motions with Prior Information Constraints [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (27 February 2009), e1000295. by Barak Raveh, Angela Enosh, Ora Schueler-Furman, Dan Halperin posted to folding motion planning protein by apaydin on 2009-03-05 19:03:00 as along with 1 person anna_yershova
	Generation, Comparison, and Merging of Pathways between Protein Conformations: Gating in K-Channels☆ [My Copy] Biophysical Journal, Vol. 95, No. 8. (15 October 2008), pp. 3850-3860. by A. Enosh, B. Raveh, O. Furmanschueler, D. Halperin, N. Bental posted to folding motion planning protein by apaydin on 2009-03-05 19:00:08 as
	Outcome of a workshop on applications of protein models in biomedical research. [My Copy] Structure (London, England : 1993), Vol. 17, No. 2. (13 February 2009), pp. 151-159. by T. Schwede, A. Sali, B. Honig, et al.M. Levitt, H. M. Berman, D. Jones, S. E. Brenner, S. K. Burley, R. Das, N. V. Dokholyan, R. L. Dunbrack, K. Fidelis, A. Fiser, A. Godzik, Y. J. Huang, C. Humblet, M. P. Jacobson, A. Joachimiak, S. R. Krystek, T. Kortemme, A. Kryshtafovych, G. T. Montelione, J. Moult, D. Murray, R. Sanchez, T. R. Sosnick, D. M. Standley, T. Stouch, S. Vajda, M. Vasquez, J. D. Westbrook, I. A. Wilson posted to modeling protein structure by apaydin on 2009-03-01 08:10:32 as
	CPSP-web-tools: a server for 3D lattice protein studies [My Copy] Bioinformatics, Vol. 25, No. 5. (1 March 2009), pp. 676-677. by Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen posted to folding lattice model protein by apaydin on 2009-02-25 19:35:46 as along with 2 people yshmte carlosjavierna
	Computational structure-based redesign of enzyme activity. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 10. (10 March 2009), pp. 3764-3769. by C. Y. Chen, I. Georgiev, A. C. Anderson, B. R. Donald posted to design protein by apaydin on 2009-02-20 16:35:50 as along with 3 people barmak7282 baiaixi zwang
	An idea whose time has gone [My Copy] Genome Biology, Vol. 8 (02 July 2007), 107. by Gregory A. Petsko posted to initiative opinion protein structure by apaydin on 2009-02-19 09:39:58 as along with 2 people dullhunk rph
	Waltzing α-helices [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1299-1300. by Victor Muñoz, Ravishankar Ramanathan posted to protein structure by apaydin on 2009-02-04 15:11:52 as along with 1 person amishp
	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
	An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem [My Copy] Advances in Artificial Intelligence (2003), pp. 993-993. by Alena Shmygelska, Holger Hoos posted to ant colony folding hp model optimization protein by apaydin on 2009-01-21 09:52:15 as
	A new algorithm for protein folding in the HP model [My Copy] In SODA '02: Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms (2002), pp. 876-884. by Alantha Newman posted to folding hp model protein by apaydin on 2009-01-21 09:43:01 as
	Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. [My Copy] Protein Eng, Vol. 16, No. 6. (June 2003), pp. 407-414. by P. Du, M. Andrec, R. M. Levy posted to fold protein space by apaydin on 2009-01-14 14:27:22 as along with 3 people karbak thaliana vavi
	Predicting Protein Folding Kinetics Via Temporal Logic Model Checking [My Copy] Algorithms in Bioinformatics (2007), pp. 252-264. by Christopher Langmead, Sumit Jha posted to folding kinetics prediction protein rate by apaydin on 2009-01-07 14:36:23 as
	1472-6807-7-50.pdf (application/pdf Object) [My Copy] by Mayr, Domingues posted to alignment protein structural by apaydin on 2009-01-07 13:27:32 as
	Understanding the Folding Rates and Folding Nuclei of Globular Proteins [My Copy] Current Protein and Peptide Science, Vol. 8, No. 6. (December 2007), pp. 521-536. by Finkelstein, V. Alexei, Ivankov, et al.N. Dmitry, Garbuzynskiy, O. Sergiy, Galzitskaya, V. Oxana posted to folding protein rate by apaydin on 2009-01-07 09:27:50 as
	Protein Structure and Its Folding Rate [My Copy] Mathematical Modelling of Biosystems (2008), pp. 273-301. by Alexei V. Finkelstein, Dmitry N. Ivankov, Sergiy O. Garbuzynskiy, Oxana V. Galzitskaya posted to folding protein rate by apaydin on 2009-01-07 09:27:32 as
	KineticDB: a database of protein folding kinetics [My Copy] Nucl. Acids Res. (8 October 2008), gkn696. by Natalya S. Bogatyreva, Alexander A. Osypov, Dmitry N. Ivankov posted to database folding kinetics protein rate by apaydin on 2009-01-07 09:25:05 as
	Direct molecular dynamics observation of protein folding transition state ensemble. [My Copy] Biophys J, Vol. 83, No. 6. (December 2002), pp. 3525-3532. by F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, E. I. Shakhnovich posted to folding pfold protein transition_state_ensemble by apaydin on 2009-01-05 10:19:50 as along with 1 person choonpeng
	Integrated search and alignment of protein structures [My Copy] Bioinformatics, Vol. 24, No. 24. (15 December 2008), pp. 2872-2879. by Ahmet Sacan, Hakki I. Toroslu, Hakan Ferhatosmanoglu posted to alignment protein structure by apaydin on 2008-12-26 07:18:21 as along with 3 people mhamada gulkur reyez
	Sampling protein conformations and pathways [My Copy] Journal of Computational Chemistry, Vol. 25, No. 9. (5 April 2004), pp. 1133-1148. by Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe posted to flexibiliy protein rigidity by apaydin on 2008-07-16 21:31:42 as along with 9 people Scis0000002 fl jrperillaj aqeel blackbart smenor ruvido nh higueruelo
	Application of the random coil index to studying protein flexibility. [My Copy] Journal of biomolecular NMR, Vol. 40, No. 1. (January 2008), pp. 31-48. by M. V. Berjanskii, D. S. Wishart posted to chemical flexibility protein shifts by apaydin on 2008-07-05 21:54:48 as
	The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts [My Copy] Nucl. Acids Res., Vol. 35, No. suppl_2. (13 July 2007), pp. W531-537. by Mark V. Berjanskii, David S. Wishart posted to chemical flexibility protein shifts webserver by apaydin on 2008-07-05 21:52:02 as along with 1 person rpetrenko
	NMR: prediction of protein flexibility. [My Copy] Nature protocols, Vol. 1, No. 2. (2006), pp. 683-688. by M. Berjanskii, D. S. Wishart posted to flexibility nmr protein by apaydin on 2008-07-05 21:44:11 as
	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
	A generative, probabilistic model of local protein structure [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8932-8937. by Wouter Boomsma, Kanti V. Mardia, Charles C. Taylor, Jesper Ferkinghoff-Borg, Anders Krogh, Thomas Hamelryck posted to prediction protein structure by apaydin on 2008-07-02 17:55:01 as along with 5 people j3xucite bertelsen biehl zwang mijam
	Protein folding: Independent unrelated pathways or predetermined pathway with optional errors [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7182-7187. by Sabrina Bedard, Mallela M. Krishna, Leland Mayne, Walter S. Englander posted to folding pathways protein by apaydin on 2008-05-21 21:49:48 as along with 1 person cactus
	Prediction of Aggregation-Prone Regions in Structured Proteins [My Copy] Journal of Molecular Biology, Vol. 380, No. 2. (04 July 2008), pp. 425-436. by Gian G. Tartaglia, Amol P. Pawar, Silvia Campioni, Christopher M. Dobson, Fabrizio Chiti, Michele Vendruscolo posted to aggregation prediction protein structure by apaydin on 2008-05-14 15:18:38 as
	Protein conformational transitions explored by mixed elastic network models. [My Copy] Proteins (27 June 2007) by Wenjun Zheng, Bernard R R. Brooks, Gerhard Hummer posted to conformational elastic folding model network protein transition by apaydin on 2008-04-17 13:45:43 as along with 2 people aqeel choonpeng
	Coarse Master Equations for Peptide Folding Dynamics [My Copy] J. Phys. Chem. B (31 January 2008) by N. V. Buchete, G. Hummer posted to dynamics equation folding master molecular protein by apaydin on 2008-04-17 13:16:30 as along with 3 people and 1 group Diego_Prada ruvido sobolevnrm baker-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
	Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target [My Copy] Journal of Structural and Functional Genomics, Vol. 5, No. 4. (25 January 2005), pp. 241-254. by H. Valafar, K. L. Mayer, C. M. Bougault, et al.P. D. Leblond, F. E. Jenney, P. S. Brereton, M. W. W. Adams, J. H. Prestegard posted to determination fragment structure based protein rdc backbone by apaydin on 2007-10-30 18:31:59 as
	Use of residual dipolar couplings as restraints in ab initio protein structure prediction. [My Copy] Biopolymers, Vol. 70, No. 4. (December 2003), pp. 548-562. by T. Haliloglu, A. Kolinski, J. Skolnick posted to lattice model prediction protein rdc structure by apaydin on 2007-10-30 18:08:24 as along with 1 person j3xucite

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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
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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
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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
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molecular_mechanics	2
native	2
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path	2
phi	2
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reference	2
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simulated	2
solvation	2
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space	2
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value	2
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xray	2
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anm	1
assembly	1
atomic	1
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belief	1
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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
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flexibiliy	1
foldamer	1
folder	1
foldtraj	1
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function_prediction	1
geometric	1
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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
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kl_distance	1
lambda	1
library	1
ligand_binding	1
linguistics	1
local	1
long	1
macromolecular	1
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maps	1
mars	1
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md	1
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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
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sequence	1
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sh3	1
simplified	1
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state	1
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structural_ensemble	1
study	1
supercomputer	1
supramolecular	1
svm	1
synthesis	1
tabu	1
task_planning	1
tensor	1
thermodynamic	1
thermodynamics	1
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topology	1
ubiquitin	1
umbrella_sampling	1
waiting_time	1
water_hsqc	1
wavelets	1
wide-angle	1

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