xdeupi's dynamics [56 articles] Export

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	Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 5. (1 February 2005), pp. 1959-1969. by Osamu Miyashita, Peter G. Wolynes, Jose N. Onuchic posted to pathways kinetics energy_landscape dynamics conformational_changes active-state activation by xdeupi on 2009-10-28 12:45:14 as along with 2 people abovell aqeel
	Asymmetric Kinetics of Protein Structural Changes [My Copy] Accounts of Chemical Research, Vol. 42, No. 6. (16 June 2009), pp. 778-787. by Stéphane Marchal, Josep Font, Marc Ribó, et al.Maria Vilanova, Robert S. Phillips, Reinhard Lange, Joan Torrent posted to pathway kinetics energy_landscape dynamics conformational_changes binding_kinetics active-state activation by xdeupi on 2009-10-28 09:14:43 as along with 1 person paulschlesinger
	Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin. [My Copy] Journal of molecular modeling, Vol. 15, No. 8. (August 2009), pp. 959-969. by Saravana Prakash P. Thirumuruganandham, Herbert M. Urbassek posted to membrane_proteins md flexibility energy_landscape dynamics disorder by xdeupi on 2009-10-25 11:22:15 as along with 2 people saravan gcaltabiano
	Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 12. (24 March 2009), pp. 4689-4694. by Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, David E. Shaw posted to theory structure modeling md flexibility dynamics b2ar activation by xdeupi on 2009-10-08 11:13:04 as along with 2 people dimka agrossfield
	Influence of the g- conformation of Ser and Thr on the structure of transmembrane helices. [My Copy] Journal of structural biology (17 September 2009) by Xavier Deupi, Mireia Olivella, Arantxa Sanz, Nicole Dölker, Mercedes Campillo, Leonardo Pardo posted to tm5 theory structure ser plasticity helix hbond flexibility dynamics amber activation by xdeupi on 2009-09-25 14:15:01 as
	The energy landscapes and motions of proteins. [My Copy] Science (New York, N.Y.), Vol. 254, No. 5038. (13 December 1991), pp. 1598-1603. by H. Frauenfelder, S. G. Sligar, P. G. Wolynes posted to theory review plasticity kinetics flexibility energy_landscape dynamics active-state activation by xdeupi on 2009-08-31 15:05:33 as along with 3 people FilipeMaia naitsabes kjell
	Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (12 August 2008), pp. 11182-11187. by Kei-ichi Okazaki, Shoji Takada posted to activation active-state dynamics energy_landscape flexibility kinetics modeling nmr plasticity theory by xdeupi on 2009-07-11 11:26:37 as along with 8 people and 2 groups oteri bmduggan okapi aqeel raik ruvido barry zwang structural_bioinformatics McCammon
	Chaos in Biomolecular Dynamics [My Copy] J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8101-8105. by H. Zhou, L. Wang posted to dynamics folding md modeling theory by xdeupi on 2009-06-08 12:28:13 as along with 1 person allmensch
	Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors. [My Copy] Biochemistry (20 April 2009) by Stefano Vanni, Marilisa Neri, Ivano Tavernelli, Ursula Rothlisberger posted to activation b2ar dry dynamics flexibility ionic lock md protonation solvation switch tm3 tm6 water by xdeupi on 2009-05-06 09:56:27 as along with 3 people and 1 group arnaucordomi jmccammon agrossfield McCammon
	Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states [My Copy] Journal of Biomolecular NMR, Vol. 41, No. 3. (1 July 2008), pp. 113-120. by D. Hansen, Pramodh Vallurupalli, Lewis Kay posted to activation active-state dynamics nmr plasticity spectroscopy structure by xdeupi on 2009-03-30 15:26:38 as along with 1 person kevinemamy
	G protein-coupled receptors show unusual patterns of intrinsic unfolding [My Copy] Protein Engineering, Design and Selection, Vol. 18, No. 2. (February 2005), pp. 103-110. by Veli-Pekka Jaakola, Jaime Prilusky, Joel L. Sussman, Adrian Goldman posted to cterm disorder dynamics flexibility folding icl3 loops modeling structure by xdeupi on 2009-03-27 09:41:46 as
	Protein Dynamics, Thermal Stability, and Free-Energy Landscapes: A Molecular Dynamics Investigation [My Copy] Vol. 85, No. 4. (1 October 2003), pp. 2641-2649. by Ivano Tavernelli, Simona Cotesta, Ernesto E. Di Iorio posted to activation dynamics flexibility md nmr ser by xdeupi on 2009-03-16 20:05:04 as
	Dynamic personalities of proteins [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972. by Katherine Henzler-Wildman, Dorothee Kern posted to activation dynamics nmr review by xdeupi on 2009-03-12 12:06:38 as along with 17 people and 1 group Diego_Prada viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
	Intrinsic motions along an enzymatic reaction trajectory. [My Copy] Nature, Vol. 450, No. 7171. (6 December 2007), pp. 838-844. by Katherine A. Henzler-Wildman, Vu Thai, Ming Lei, et al.Maria Ott, Magnus Wolf-Watz, Tim Fenn, Ed Pozharski, Mark A. Wilson, Gregory A. Petsko, Martin Karplus, Christian G. Hübner, Dorothee Kern posted to nmr energy_landscape dynamics activation by xdeupi on 2009-03-12 12:01:52 as along with 11 people and 1 group ahmetbakan ubcg08l ruvido barry aqeel ebeutler cactus sobolevnrm paulschlesinger jlh64 yalexeev baker-group
	Functional dynamics of response regulators using NMR relaxation techniques. [My Copy] Methods in enzymology, Vol. 423 (2007), pp. 149-165. by A. K. Gardino, D. Kern posted to activation dynamics nmr by xdeupi on 2009-03-12 11:51:30 as
	The role of dynamics in allosteric regulation [My Copy] Current Opinion in Structural Biology, Vol. 13, No. 6. (December 2003), pp. 748-757. by Dorothee Kern, Erik R. P. Zuiderweg posted to activation dynamics by xdeupi on 2009-03-12 11:17:35 as along with 1 person jlh64
	Automation of NMR structure determination of proteins. [My Copy] Curr Opin Struct Biol, Vol. 14, No. 5. (October 2004), pp. 547-553. by A. S. Altieri, R. A. Byrd posted to dynamics nmr review structure by xdeupi on 2009-03-10 15:30:11 as along with 2 people kumar_physics apaydin
	Extensive Backbone Dynamics in the GCAA RNA Tetraloop Analyzed Using 13C NMR Spin Relaxation and Specific Isotope Labeling [My Copy] Journal of the American Chemical Society, Vol. 130, No. 49. (10 December 2008), pp. 16757-16769. by James E. Johnson, Charles G. Hoogstraten posted to dynamics nmr by xdeupi on 2009-03-10 15:03:00 as
	Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 33. (19 August 2008), pp. 11766-11771. by P. Vallurupalli, D. F. Hansen, L. E. Kay posted to dynamics nmr by xdeupi on 2009-03-10 14:59:11 as
	Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy. [My Copy] Journal of the American Chemical Society, Vol. 131, No. 5. (11 February 2009), pp. 1915-1926. by P. Lundström, D. F. Hansen, P. Vallurupalli, L. E. Kay posted to dynamics nmr by xdeupi on 2009-03-10 14:51:57 as
	Simultaneous determination of protein structure and dynamics [My Copy] Nature, Vol. 433, No. 7022. (13 January 2005), pp. 128-132. by Kresten Lindorff-Larsen, Robert B. Best, Mark A. Depristo, Christopher M. Dobson, Michele Vendruscolo posted to dynamics nmr structure by xdeupi on 2009-03-10 14:48:36 as along with 15 people and 3 groups Diego_Prada A_Coletta_Thesis karbak apaydin barry lillekatt baaden lna dgront allmensch daevans rsantana jlh64 biehl rph Structural Biology Group TorVergata structural_bioinformatics Bioinformatics
	New Tools Provide New Insights in NMR Studies of Protein Dynamics [My Copy] Science, Vol. 312, No. 5771. (14 April 2006), pp. 224-228. by Anthony Mittermaier, Lewis E. Kay posted to activation dynamics nmr review by xdeupi on 2009-03-10 14:43:09 as along with 5 people bmduggan apaydin lna aqeel laurabailey
	Development and testing of a general amber force field. [My Copy] J Comput Chem, Vol. 25, No. 9. (15 July 2004), pp. 1157-1174. by J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case posted to amber dynamics md theory by xdeupi on 2007-06-26 13:51:26 as along with 10 people and 1 group rdf paddydu nigham lillekatt gane5h kazemi megs easybakemuffin AndreaColetta pavanghatty LabCompMed
	Performance of the general amber force field in modeling aqueous POPC membrane bilayers [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058. by Balázs Jójárt, Tamás A. Martinek posted to amber dynamics md membrane modeling theory by xdeupi on 2007-06-26 13:32:45 as along with 3 people and 1 group dimka easybakemuffin viktor21614 LabCompMed
	Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. [My Copy] J Comput Chem (31 January 2007) by Arnau Cordomí, Olle Edholm, Juan J J. Perez posted to dynamics md membrane rhodopsin theory by xdeupi on 2007-06-25 10:30:55 as along with 2 people and 1 group patricia arnaucordomi LabCompMed
	An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies [My Copy] Protein Eng., Vol. 9, No. 11. (1996), pp. 1063-1065. by Lawrence A. Kelley, Stephen P. Gardner, Michael J. Sutcliffe posted to dynamics helix md modeling structure theory by xdeupi on 2007-05-31 10:31:28 as along with 1 group LabCompMed
	Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package. [My Copy] J Phys Chem A (24 May 2007) by Gustavo D. Seabra, Ross C. Walker, Marcus Elstner, David A. Case, Adrian E. Roitberg posted to amber dynamics theory by xdeupi on 2007-05-28 08:54:09 as along with 3 people and 1 group krapnik charris5 vahmurk LabCompMed
	Protein flexibility using constraints from molecular dynamics simulations. [My Copy] Phys Biol, Vol. 2, No. 4. (November 2005) by T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. Kurnikova posted to activation dynamics flexibility md by xdeupi on 2007-05-21 09:38:21 as along with 3 people and 1 group lna LamBras higueruelo LabCompMed
	Determining membrane protein structures: still a challenge! [My Copy] Trends Biochem Sci (2 May 2007) by Jean-Jacques J. Lacapère, Eva Pebay-Peyroula, Jean-Michel M. Neumann, Catherine Etchebest posted to crystallography dynamics membrane_proteins nmr review structure by xdeupi on 2007-05-15 12:52:21 as along with 1 person and 1 group gcaltabiano LabCompMed
	Synthesis of TOAC spin-labeled proteins and reconstitution in lipid membranes. [My Copy] Nat Protoc, Vol. 2, No. 1. (2007), pp. 42-49. by C. B. Karim, Z. Zhang, D. D. Thomas posted to dynamics gpcr toac by xdeupi on 2007-04-10 19:30:43 as along with 1 group LabCompMed
	Modeling activated states of GPCRs: the rhodopsin template. [My Copy] J Comput Aided Mol Des, Vol. 20, No. 7-8. (g 2006), pp. 437-448. by M. Y. Niv, L. Skrabanek, M. Filizola, H. Weinstein posted to activation dynamics md rhodopsin by xdeupi on 2007-03-26 10:22:13 as along with 1 person and 1 group IrinaMoreira LabCompMed
	Setting up and running molecular dynamics simulations of membrane proteins. [My Copy] Methods (San Diego, Calif.), Vol. 41, No. 4. (April 2007), pp. 475-488. by Christian Kandt, Walter L. Ash, D. Peter Tieleman posted to dynamics md membrane modeling review transmembrane by xdeupi on 2007-03-26 10:15:17 as along with 3 people and 2 groups arnaucordomi choonpeng sobolevnrm LabCompMed baker-group
	Structure and conformational changes in the C-terminal domain of the beta 2-adrenoceptor: Insights from fluorescence resonance energy tranfer studies. [My Copy] J Biol Chem (8 March 2007) by Sebastien Granier, Samuel Kim, Aaron M M. Shafer, et al.Venkata R P R. Ratnala, Juan J J. Fung, Richard N N. Zare, Brian K K. Kobilka posted to activation b2ar cterm dynamics fret structure by xdeupi on 2007-03-21 11:39:56 as along with 1 group LabCompMed
	Two-dimensional solid-state NMR applied to a chimeric potassium channel. [My Copy] J Recept Signal Transduct Res, Vol. 26, No. 5-6. (2006), pp. 379-393. by A. Lange, K. Giller, O. Pongs, S. Becker, M. Baldus posted to channel dynamics membrane_proteins nmr structure by xdeupi on 2007-03-12 14:23:33 as along with 1 group LabCompMed
	Molecular dynamics simulation of the human adenosine A3 receptor: agonist induced conformational changes of Trp243 [My Copy] Journal of Computer-Aided Molecular Design, Vol. 20, No. 10-11. (October 2006), pp. 673-684. by Hallmen, Christian, Wiese, Michael posted to dynamics lipids md membrane by xdeupi on 2007-03-12 14:22:10 as along with 1 group LabCompMed
	Predisposition of the dark state of rhodopsin to functional changes in structure [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 4. (2006), pp. 970-983. by Basak Isin, A. J. Rader, Harpreet K. Dhiman, Judith Klein-Seetharaman, Ivet Bahar posted to activation dynamics modeling rhodopsin by xdeupi on 2007-02-26 09:19:19 as along with 1 person and 1 group aqeel LabCompMed
	How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. [My Copy] Proteins, Vol. 66, No. 3. (15 February 2007), pp. 559-574. by P. S. Crozier, M. J. Stevens, T. B. Woolf posted to activation dynamics md modeling rhodopsin switch by xdeupi on 2007-02-26 09:15:15 as along with 1 group LabCompMed
	A methyl group at C7 of 11-cis-retinal allows chromophore formation but affects rhodopsin activation. [My Copy] Vision Res (5 October 2006) by Laia Bosch, Arnau Cordomí, Marta Domínguez, et al.Darwin Toledo, Margarita Morillo, Juan J J. Pérez, Rosana Alvarez, Angel R R. de Lera, Pere Garriga posted to activation dynamics md rhodopsin by xdeupi on 2007-02-20 09:56:24 as along with 1 person and 1 group arnaucordomi LabCompMed
	Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data. [My Copy] Protein Sci, Vol. 15, No. 11. (November 2006), pp. 2544-2551. by D. Trzesniak, W. F. van Gunsteren posted to crystallography dynamics modeling by xdeupi on 2007-02-20 09:52:40 as along with 1 group LabCompMed
	A change in conformational dynamics underlies the activation of Eph receptor tyrosine kinases [My Copy] The EMBO Journal, Vol. aop, No. current. (14 September 2006) by Silke Wiesner, Leanne E. Wybenga-Groot, Neil Warner, et al.Hong Lin, Tony Pawson, Julie D. Forman-Kay, Frank Sicheri posted to activation crystallography dynamics mutation nmr switch by xdeupi on 2006-11-17 20:55:01 as along with 1 group LabCompMed
	Dynamic helix interactions in transmembrane signaling. [My Copy] Cell, Vol. 127, No. 3. (3 November 2006), pp. 447-450. by E. E. Matthews, M. Zoonens, D. M. Engelman posted to activation dynamics helix review transmembrane by xdeupi on 2006-11-14 16:44:32 as along with 2 people and 1 group gcaltabiano ndoelker LabCompMed
	Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. [My Copy] J Comput Aided Mol Des (7 November 2006) by Marta Filizola, Simon X. Wang, Harel Weinstein posted to activation dynamics gpcr lipids md membrane rhodopsin structure by xdeupi on 2006-11-14 16:42:29 as along with 1 group LabCompMed
	A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations. [My Copy] Biophys J, Vol. 91, No. 7. (1 October 2006), pp. 2647-2664. by C. Beier, H. J. Steinhoff posted to dynamics loops md modeling spin_labeling structure by xdeupi on 2006-10-30 18:37:07 as along with 1 group LabCompMed
	dummy [My Copy] by Dummy posted to 5ht1a activation agonist amber amine arrestin b2ar bimane binding cam ccr5 channel chemokine chimera crystallography cterm cxcr1 d250 dimer disease drug dry dynamics ecl2 evolution expression fluorescence folding fret genome gly gpcr gproteins hbond helix helix8 histamine hormone icl3 imaging internalization ionic leukotriene lhr ligands lipids lock loops md membrane modeling mutation n745 n749 nmr npxxy nterm opioid pharmacology polymorphism pro-kink protonation review rhodopsin s542 sequence ser spin_labeling structure switch thr thyrotropin tm2 tm3 tm5 tm6 tm7 toggle transmembrane trp txp w648 by xdeupi on 2006-10-30 12:30:16 as along with 2 people and 1 group jessicaopacic ivanrt LabCompMed
	Asymmetric stability among the transmembrane helices of lactose permease. [My Copy] Biochemistry, Vol. 45, No. 26. (4 July 2006), pp. 8088-8095. by M. Bennett, R. D'Rozario, M. S. Sansom, P. L. Yeagle posted to activation dynamics helix md modeling structure transmembrane by xdeupi on 2006-09-05 11:09:02 as along with 1 group LabCompMed
	Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry. [My Copy] Protein Sci, Vol. 15, No. 6. (June 2006), pp. 1303-1317. by R. B. Jacobsen, K. L. Sale, M. J. Ayson, et al.P. Novak, J. Hong, P. Lane, N. L. Wood, G. H. Kruppa, M. M. Young, J. S. Schoeniger posted to dynamics gpcr modeling rhodopsin structure by xdeupi on 2006-09-05 10:52:14 as along with 1 group LabCompMed
	Bridging conformational dynamics and function using single-molecule spectroscopy. [My Copy] Structure, Vol. 14, No. 4. (April 2006), pp. 633-643. by S. Myong, B. C. Stevens, T. Ha posted to dynamics fluorescence imaging structure by xdeupi on 2006-07-24 11:01:22 as along with 1 group LabCompMed
	Molecular Dynamics Simulations of GlpF in a Micelle vs in a Bilayer: Conformational Dynamics of a Membrane Protein as a Function of Environment. [My Copy] J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 109, No. 1. (13 January 2005), pp. 575-582. by G. Patargias, P. J. Bond, S. S. Deol, M. S. Sansom posted to crystallography dynamics membrane structure transmembrane by xdeupi on 2006-07-24 10:25:16 as along with 1 person and 1 group paulschlesinger LabCompMed
	Picosecond dynamics of G-protein coupled receptor activation in rhodopsin from time-resolved UV resonance Raman spectroscopy. [My Copy] Biochemistry, Vol. 42, No. 18. (13 May 2003), pp. 5169-5175. by J. E. Kim, D. Pan, R. A. Mathies posted to activation dynamics fluorescence rhodopsin switch thyrotropin toggle w648 by xdeupi on 2006-06-02 12:33:11 as along with 1 group LabCompMed
	The role of extra-membranous inter-helical loops in helix-helix interactions. [My Copy] Protein Eng Des Sel, Vol. 18, No. 12. (December 2005), pp. 563-570. by M. B. Ulmschneider, D. P. Tieleman, M. S. Sansom posted to dynamics helix loops md membrane transmembrane by xdeupi on 2006-03-06 09:46:32 as along with 2 people and 1 group thaliana allanlo LabCompMed

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activation	171
gpcr	110
structure	89
rhodopsin	79
review	64
modeling	62
b2ar	58
dynamics	56
helix	50
transmembrane	47
agonist	46
binding	44
theory	42
ligands	41
drug	36
md	35
switch	34
membrane_proteins	31
crystallography	30
nmr	30
pharmacology	30
membrane	26
gproteins	23
dimer	20
fluorescence	18
sequence	17
ser	17
active-state	15
folding	14
fret	14
genome	14
loops	14
pro-kink	14
flexibility	13
disease	12
tm6	12
cterm	11
mutation	11
retinal	11
amber	10
evolution	10
toggle	10
docking	9
energy_landscape	9
kinetics	9
lipids	9
neurokinin	9
tm5	9
arrestin	8
chemokine	8
gpcrs	8
hbond	8
helix8	8
imaging	8
bimane	7
cancer	7
channel	7
ecl2	7
gly	7
icl3	7
ionic	7
lmc_101	7
plasticity	7
protonation	7
tm3	7
w648	7
cation-pi	6
ccr5	6
cys_scanning	6
d250	6
internalization	6
npxxy	6
opioid	6
thyrotropin	6
tm2	6
xray	6
amine	5
binding_kinetics	5
conformational_changes	5
dimerization	5
dry	5
expression	5
lock	5
polymorphism	5
spectroscopy	5
thr	5
trp	5
antagonist	4
cam	4
cholesterol	4
disorder	4
hormone	4
n749	4
nterm	4
pathway	4
tm7	4
water	4
angiotensin	3
biased_agonism	3
cxcr1	3
grk	3
histamine	3
n745	3
oligomerization	3
spin_labeling	3
toac	3
webserver	3
5ht1a	2
chimera	2
crosslinking	2
em	2
leukotriene	2
lhr	2
networks	2
pathways	2
phylogeny	2
s542	2
solvation	2
tm1	2
tmhs	2
txp	2
b1ar	1
binding_site	1
class_c	1
efficacy	1
gaba	1
induced_fit	1
inverse_agonist	1
kinase	1
kinks	1
metai	1
oligomers	1
peptide	1
priviledged_structures	1
proline	1
protein_docking	1
sequence_alignment	1
tm4	1
transducin	1
vasopressin	1

xdeupi's dynamics [56 articles] Export

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