xdeupi's modeling [62 articles] Export

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	Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use? [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 16. (27 August 2009), pp. 5207-5216. by Juan C. Mobarec, Roberto Sanchez, Marta Filizola posted to theory modeling gpcr docking by xdeupi on 2009-10-08 16:39:12 as along with 2 people dimka reyez
	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
	Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists. [My Copy] Proteins (12 August 2009) by Brajesh K. Rai, Gregory J. Tawa, Alan H. Katz, Christine Humblet posted to theory modeling md gpcr by xdeupi on 2009-10-06 19:31:07 as
	Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. [My Copy] PloS one, Vol. 4, No. 9. (2009) by Catherine L. Worth, Gunnar Kleinau, Gerd Krause posted to structure sequence review modeling gpcr by xdeupi on 2009-10-06 19:24:07 as
	Structural and kinetic modeling of an activating helix switch in the rhodopsin-transducin interface. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 26. (30 June 2009), pp. 10660-10665. by Patrick Scheerer, Martin Heck, Andrean Goede, et al.Jung Hee H. Park, Hui-Woog W. Choe, Oliver P. Ernst, Klaus Peter P. Hofmann, Peter W. Hildebrand posted to transducin switch structure rhodopsin modeling kinetics helix activation by xdeupi on 2009-10-06 18:16:43 as
	Homology modeling of GPCRs. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 552 (2009), pp. 97-113. by John Simms, Nathan E. Hall, Polo H. Lam, et al.Laurence J. Miller, Arthur Christopoulos, Ruben Abagyan, Patrick M. Sexton posted to theory review modeling gpcr by xdeupi on 2009-10-06 18:14:40 as
	New vistas in GPCR 3D structure prediction [My Copy] Journal of Molecular Modeling by Anwar Rayan posted to theory sequence_alignment sequence modeling gpcr by xdeupi on 2009-10-06 17:47:03 as along with 1 person arnaucordomi
	A model for the solution structure of the rod arrestin tetramer. [My Copy] Structure (London, England : 1993), Vol. 16, No. 6. (June 2008), pp. 924-934. by Susan M. Hanson, Eric S. Dawson, Derek J. Francis, et al.Ned Van Eps, Candice S. Klug, Wayne L. Hubbell, Jens Meiler, Vsevolod V. Gurevich posted to modeling docking arrestin by xdeupi on 2009-10-05 18:41:01 as
	Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies [My Copy] Journal of Molecular Modeling by Gilles Pieffet, Pavel Petukhov posted to theory spectroscopy modeling md fluorescence amber by xdeupi on 2009-09-15 14:25:43 as
	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
	Sequence-Derived Three-Dimensional Pharmacophore Models for G-Protein-Coupled Receptors and Their Application in Virtual Screening [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by Thomas Klabunde, Clemens Giegerich, Andreas Evers posted to agonist antagonist binding drug ligands modeling pharmacology by xdeupi on 2009-05-06 09:59:59 as along with 1 person reyez
	Revisiting Automated G-Protein Coupled Receptor Modeling: The Benefit of Additional Template Structures for a Neurokinin-1 Receptor Model. [My Copy] Journal of medicinal chemistry (28 April 2009) by Benny Kneissl, Bettina Leonhardt, Andreas Hildebrandt, Christofer S S. Tautermann posted to docking gpcr ligands modeling neurokinin by xdeupi on 2009-05-06 09:47:25 as along with 1 person reyez
	Wide turn diversity in protein transmembrane helices implications for G-protein-coupled receptor and other polytopic membrane protein structure and function. [My Copy] Molecular pharmacology, Vol. 73, No. 4. (April 2008), pp. 1092-1104. by R. Peter Riek, Angela A. Finch, Gillian E. Begg, Robert M. Graham posted to flexibility helix membrane_proteins modeling pro-kink ser structure theory thr transmembrane by xdeupi on 2009-04-17 11:47:42 as
	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
	Activation of the mu opioid receptor involves conformational rearrangements of multiple transmembrane domains. [My Copy] Biochemistry, Vol. 47, No. 40. (7 October 2008), pp. 10576-10586. by W. Xu, A. Sanz, L. Pardo, L. Y. Liu-Chen posted to activation cys_scanning modeling opioid switch by xdeupi on 2008-10-15 10:57:26 as
	The specificity of binding of glycoprotein hormones to their receptors. [My Copy] Cellular and molecular life sciences : CMLS (26 April 2008) by G Caltabiano, M Campillo, A De Leener, et al.G Smits, G Vassart, S Costagliola, L Pardo posted to activation hormone modeling thyrotropin by xdeupi on 2008-05-03 17:06:33 as along with 1 group LabCompMed
	Protein-Protein Docking with Backbone Flexibility [My Copy] Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519. by Chu Wang, Philip Bradley, David Baker posted to docking flexibility modeling theory by xdeupi on 2008-04-07 14:23:45 as along with 6 people and 2 groups mijam kgutwin csrocha barry jwm Ema structural_bioinformatics Bioinformatics
	Protein-Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations [My Copy] Journal of Molecular Biology, Vol. 331, No. 1. (1 August 2003), pp. 281-299. by Jeffrey J. Gray, Stewart Moughon, Chu Wang, et al.Ora Schueler-Furman, Brian Kuhlman, Carol A. Rohl, David Baker posted to dimer docking modeling theory by xdeupi on 2008-04-07 14:18:56 as along with 4 people ima bluvsh1 selrac timg
	A concept for G protein activation by G protein-coupled receptor dimers: the transducin/rhodopsin interface. [My Copy] Photochem Photobiol Sci, Vol. 3, No. 6. (June 2004), pp. 628-638. by S. Filipek, K. A. Krzysko, D. Fotiadis, et al.Y. Liang, D. A. Saperstein, A. Engel, K. Palczewski posted to active-state gproteins modeling rhodopsin structure by xdeupi on 2007-07-11 16:54:09 as along with 1 person and 1 group cen4ik LabCompMed
	Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites. [My Copy] Biochemistry, Vol. 43, No. 27. (13 July 2004), pp. 8700-8710. by C. B. Fowler, I. D. Pogozheva, H. LeVine, H. I. Mosberg posted to active-state modeling opioid structure theory by xdeupi on 2007-07-11 16:51:53 as along with 1 person and 1 group merj LabCompMed
	Complex of an active mu-opioid receptor with a cyclic peptide agonist modeled from experimental constraints. [My Copy] Biochemistry, Vol. 43, No. 50. (21 December 2004), pp. 15796-15810. by C. B. Fowler, I. D. Pogozheva, A. L. Lomize, H. LeVine, H. I. Mosberg posted to active-state gproteins modeling opioid structure by xdeupi on 2007-07-11 16:50:15 as along with 1 group LabCompMed
	Modeling of the complex between transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor. [My Copy] Biochemistry, Vol. 46, No. 16. (24 April 2007), pp. 4734-4744. by G. V. Nikiforovich, C. M. Taylor, G. R. Marshall posted to gproteins modeling rhodopsin by xdeupi on 2007-07-11 11:05:58 as along with 1 group 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
	Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting [My Copy] Journal of Molecular Biology, Vol. 357, No. 5. (14 April 2006), pp. 1655-1668. by Maya Topf, Matthew L. Baker, Marc A. Marti-Renom, Wah Chiu, Andrej Sali posted to crystallography em modeling structure theory by xdeupi on 2007-06-12 11:28:16 as along with 1 group 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
	Structural models of class a g protein-coupled receptors as a tool for drug design: insights on transmembrane bundle plasticity. [My Copy] Curr Top Med Chem, Vol. 7, No. 10. (2007), pp. 999-1006. by X. Deupi, N. Dölker, M. L. López-Rodríguez, M. Campillo, J. A. Ballesteros, L. Pardo posted to binding gpcr modeling plasticity structure by xdeupi on 2007-05-28 08:51:54 as along with 1 group LabCompMed
	Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin. [My Copy] J Am Chem Soc (15 May 2007) by Ting Wang, Yong Duan posted to activation agonist amber binding ligands md modeling rhodopsin by xdeupi on 2007-05-21 10:04:04 as along with 1 group LabCompMed
	Computational prediction of atomic structures of helical membrane proteins aided by EM maps. [My Copy] Biophys J (11 May 2007) by Julio A A. Kovacs, Mark Yeager, Ruben Abagyan posted to crystallography em membrane_proteins modeling structure by xdeupi on 2007-05-21 09:41:00 as along with 1 person and 1 group thaliana LabCompMed
	Understanding interactions of gastric inhibitory polypeptide (GIP) with its G-protein coupled receptor through NMR and molecular modeling. [My Copy] J Pept Sci, Vol. 13, No. 5. (16 April 2007), pp. 287-300. by Alpeshkumar K K. Malde, Sudha S S. Srivastava, Evans C C. Coutinho posted to modeling nmr nterm by xdeupi on 2007-04-23 10:26:25 as along with 1 group LabCompMed
	Peptide design and structural characterization of a GPCR loop mimetic. [My Copy] Biopolymers (18 April 2007) by Truc-Chi T C. Pham, Richard W W. Kriwacki, Abby L L. Parrill posted to gpcr loops modeling structure by xdeupi on 2007-04-23 10:24:23 as along with 1 group LabCompMed
	Pharmacogenomic and structural analysis of constitutive g protein-coupled receptor activity. [My Copy] Annu Rev Pharmacol Toxicol, Vol. 47 (2007), pp. 53-87. by M. J. Smit, H. F. Vischer, R. A. Bakker, et al.A. Jongejan, H. Timmerman, L. Pardo, R. Leurs posted to activation disease gpcr modeling review structure switch by xdeupi on 2007-04-17 12:35:15 as along with 1 group LabCompMed
	Atomic-level characterization of disordered protein ensembles [My Copy] Current Opinion in Structural Biology In Folding and binding / Protein-nucleic interactions, Vol. 17, No. 1. (February 2007), pp. 3-14. by Tanja Mittag, Julie D. Forman-Kay posted to crystallography cterm disorder folding icl3 modeling nmr structure by xdeupi on 2007-03-27 16:17:12 as along with 6 people and 1 group yxue flbarroso apaydin cactus biehl allmensch LabCompMed
	Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling. [My Copy] J Comput Aided Mol Des, Vol. 20, No. 7-8. (g 2006), pp. 449-461. by F. Fanelli, P. G. De Benedetti posted to gpcr modeling review by xdeupi on 2007-03-26 10:31:45 as along with 1 group 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
	Method To Assess Packing Quality of Transmembrane alpha-Helices in Proteins. 1. Parametrization Using Structural Data. [My Copy] J Chem Inf Model (20 March 2007) by Anton O. Chugunov, Valery N. Novoseletsky, Dmitry E. Nolde, Alexander S. Arseniev, Roman G. Efremov posted to gpcr membrane_proteins modeling structure by xdeupi on 2007-03-26 10:07:02 as along with 1 person and 1 group superpyrin 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
	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
	Solvation parameters for amino acids [My Copy] Journal of Computational Chemistry, Vol. 20, No. 4. (1999), pp. 428-442. by Brian J. Smith posted to solvation modeling by xdeupi on 2007-01-12 12:48:19 as along with 1 person and 1 group papatonyhill LabCompMed
	GluVII:06--a highly conserved and selective anchor point for non-peptide ligands in chemokine receptors. [My Copy] Curr Top Med Chem, Vol. 6, No. 13. (2006), pp. 1319-1333. by M. M. Rosenkilde, T. W. Schwartz posted to modeling ligands ionic chemokine binding agonist by xdeupi on 2007-01-10 14:45:13 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
	Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor. [My Copy] J Comput Aided Mol Des (13 October 2006) by Stanley R. Krystek, S R. Kimura, Andrew J. Tebben posted to b2ar binding drug ligands modeling pharmacology by xdeupi on 2006-10-27 09:43:03 as along with 1 person and 1 group daevans LabCompMed
	Helix-packing motifs in membrane proteins. [My Copy] Proc Natl Acad Sci U S A (5 September 2006) by R F S F. Walters, W F F. Degrado posted to folding helix membrane modeling sequence structure transmembrane by xdeupi on 2006-09-13 10:25:08 as along with 5 people and 1 group hc5428 thaliana dgront sebk chgjb 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
	Novel mutants of the human beta1-adrenergic receptor reveal amino acids relevant for receptor activation. [My Copy] J Biol Chem, Vol. 281, No. 26. (30 June 2006), pp. 18120-18125. by B. Behr, C. Hoffmann, G. Ottolina, K. N. Klotz posted to activation agonist b2ar binding drug ligands modeling mutation pharmacology structure by xdeupi on 2006-09-05 11:05:20 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
	ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins. [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006) by E. Granseth, H. Viklund, A. Elofsson posted to helix loops membrane modeling structure transmembrane by xdeupi on 2006-09-05 10:16:39 as along with 2 people and 1 group thaliana chrn LabCompMed
	TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations [My Copy] Journal of Computer-Aided Molecular Design, Vol. 20, No. 2. (February 2006), pp. 97-107. by Mezei, Mihaly, Filizola, Marta posted to md modeling structure transmembrane by xdeupi on 2006-07-21 12:20:38 as along with 1 group LabCompMed

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activation	173
gpcr	112
structure	89
rhodopsin	79
review	65
modeling	62
b2ar	58
dynamics	56
helix	50
transmembrane	47
agonist	46
binding	44
theory	43
ligands	41
drug	36
md	35
switch	34
membrane_proteins	31
pharmacology	31
crystallography	30
nmr	30
membrane	26
gproteins	24
dimer	20
fluorescence	18
sequence	17
ser	17
active-state	15
pro-kink	15
folding	14
fret	14
genome	14
loops	14
flexibility	13
disease	12
tm6	12
cterm	11
mutation	11
retinal	11
amber	10
energy_landscape	10
evolution	10
toggle	10
docking	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
protein_docking	1
selectivity	1
sequence_alignment	1
tm4	1
transducin	1
vasopressin	1

xdeupi's modeling [62 articles] Export

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