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xdeupi's structure [70 articles]

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  • Investigation of transmembrane proteins using a computational approach.
    BMC genomics, Vol. 9 Suppl 1 (2008)
    by JY Yang, MQ Yang, AK Dunker, Y Deng, X Huang
    posted to transmembrane theory structure membrane_proteins loops gpcr disorder by xdeupi on 2008-10-20 22:23:57 as **
  • The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist
    Science (2 October 2008), 1164772.
    by Veli-Pekka Jaakola, Mark T Griffith, Michael A Hanson, Vadim Cherezov, Ellen Y Chien, Robert J Lane, Adriaan P Ijzerman, Raymond C Stevens
    posted to xray structure ligands gpcr docking crystallography binding by xdeupi on 2008-10-15 10:02:26 as ** along with 1 person and 1 group cen4ik LabCompMed
  • Structure of a β1-adrenergic G-protein-coupled receptor
    Nature (25 June 2008)
    by Tony Warne, Maria J Serrano-Vega, Jillian G Baker, Rouslan Moukhametzianov, Patricia C Edwards, Richard Henderson, Andrew GW Leslie, Christopher G Tate, Gebhard FX Schertler
    posted to xray structure ligands drug docking binding b2ar by xdeupi on 2008-09-16 10:15:17 as ** along with 2 people and 2 groups merj TonyIvetac LabCompMed McCammon
  • Proline-induced distortions of transmembrane helices.
    J Mol Biol, Vol. 323, No. 5. (8 November 2002), pp. 951-960.
    by FS Cordes, JN Bright, MS Sansom
    posted to activation helix membrane_proteins pro-kink structure theory transmembrane by xdeupi on 2008-05-27 11:58:27 as ** along with 1 person thaliana
  • Analysis of side-chain rotamers in transmembrane proteins.
    Biophysical journal, Vol. 87, No. 5. (November 2004), pp. 3460-3469.
    by AK Chamberlain, JU Bowie
    posted to flexibility hbond helix membrane_proteins ser serthr_paper structure thr transmembrane by xdeupi on 2008-05-15 11:35:47 as ** along with 1 person and 1 group carlk LabCompMed
  • Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region.
    The Journal of biological chemistry (6 May 2008)
    by Tatsuro Shimamura, Kenji Hiraki, Naoko Takahashi, Tetsuya Hori, Hideo Ago, Katsuyoshi Masuda, Koji Takio, Masaji Ishiguro, Masashi Miyano
    posted to crystallography cterm gpcr rhodopsin structure xray by xdeupi on 2008-05-13 16:19:24 as ** along with 1 group LabCompMed
  • Transmembrane helix uniformity examined by spectral mapping of torsion angles.
    Structure (London, England : 1993), Vol. 16, No. 5. (May 2008), pp. 787-797.
    by RC Page, S Kim, TA Cross
    posted to hbond helix structure transmembrane by xdeupi on 2008-05-13 16:04:28 as **
  • Uniformity, ideality, and hydrogen bonds in transmembrane alpha-helices.
    Biophysical journal, Vol. 83, No. 4. (October 2002), pp. 2084-2095.
    by S Kim, TA Cross
    posted to flexibility hbond helix retinal_binding_proteins structure transmembrane by xdeupi on 2008-05-13 16:00:40 as **
  • Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
    Q Rev Biophys, Vol. 37, No. 2. (May 2004), pp. 121-146.
    by U Lehnert, Y Xia, TE Royce, CS Goh, Y Liu, A Senes, H Yu, ZL Zhang, DM Engelman, M Gerstein
    posted to membrane_proteins review serthr_paper structure theory transmembrane by xdeupi on 2008-05-01 19:11:17 as ***** along with 1 person thaliana
  • Stable Interactions Between the Transmembrane Domains of the Adenosine A2A Receptor.
    Protein science : a publication of the Protein Society (23 April 2008)
    by Damien Thevenin, Tzvetana Lazarova
    posted to folding gpcr structure transmembrane by xdeupi on 2008-04-28 11:00:29 as ** along with 1 person IrinaMoreira
  • notes Transmembrane proteins in the Protein Data Bank: identification and classification.
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 2964-2972.
    by GE Tusnády, Z Dosztányi, I Simon
    posted to structure membrane_proteins lmc_101 helix by xdeupi on 2008-04-08 13:55:52 as ** along with 4 people and 1 group kallberg chrn sebk viktor21614 LabCompMed
  • Retinylidene proteins: structures and functions from archaea to humans.
    Annual review of cell and developmental biology, Vol. 16 (2000), pp. 365-392.
    by JL Spudich, CS Yang, KH Jung, EN Spudich
    posted to retinal retinal_binding_proteins review rhodopsin structure by xdeupi on 2008-04-08 11:33:18 as ** along with 1 group LabCompMed
  • Crystal structure of rhodopsin: implications for vision and beyond.
    Current opinion in structural biology, Vol. 11, No. 4. (August 2001), pp. 420-426.
    by T Okada, K Palczewski
    posted to retinal retinal_binding_proteins review rhodopsin structure by xdeupi on 2008-04-08 11:29:02 as ** along with 1 group LabCompMed
  • The relation between the divergence of sequence and structure in proteins.
    EMBO J, Vol. 5, No. 4. (April 1986), pp. 823-826.
    by C Chothia, AM Lesk
    posted to sequence structure theory by xdeupi on 2008-04-02 15:48:23 as ** along with 7 people and 6 groups ana pansapiens jwm Einat marcius ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
  • A concept for G protein activation by G protein-coupled receptor dimers: the transducin/rhodopsin interface.
    Photochem Photobiol Sci, Vol. 3, No. 6. (June 2004), pp. 628-638.
    by S Filipek, KA Krzysko, D Fotiadis, Y Liang, DA 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.
    Biochemistry, Vol. 43, No. 27. (13 July 2004), pp. 8700-8710.
    by CB Fowler, ID Pogozheva, H LeVine, HI 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.
    Biochemistry, Vol. 43, No. 50. (21 December 2004), pp. 15796-15810.
    by CB Fowler, ID Pogozheva, AL Lomize, H LeVine, HI Mosberg
    posted to active-state gproteins modeling opioid structure by xdeupi on 2007-07-11 16:50:15 as ** along with 1 group LabCompMed
  • Formation of Transmembrane Helices In Vivo--Is Hydrophobicity All that Matters?
    J. Gen. Physiol., Vol. 129, No. 5. (30 April 2007), pp. 353-356.
    by Gunnar von Heijne
    posted to helix membrane_proteins review structure transmembrane by xdeupi on 2007-06-29 21:20:58 as ** along with 2 people and 1 group hc5428 thaliana LabCompMed
  • Critical role for the second extracellular loop in the binding of both orthosteric and allosteric G protein-coupled receptor ligands.
    J Biol Chem (25 June 2007)
    by Vimesh A A Avlani, Karen J J Gregory, Craig J J Morton, Michael W W Parker, Patrick M M Sexton, Arthur Christopoulos
    posted to activation binding ecl2 ligands loops structure by xdeupi on 2007-06-29 21:12:42 as ** along with 1 group LabCompMed
  • G-protein-coupled receptor signalling through protein networks.
    Biochem Soc Trans, Vol. 35, No. Pt 1. (February 2007), pp. 23-27.
    by AD Strosberg, C Nahmias
    posted to b2ar gpcr pharmacology review structure by xdeupi on 2007-06-29 21:10:57 as ** along with 1 group LabCompMed
  • Comparison of stability predictions and simulated unfolding of rhodopsin structures.
    Photochem Photobiol, Vol. 83, No. 2. (r 2007), pp. 351-363.
    by O Tastan, E Yu, M Ganapathiraju, A Aref, AJ Rader, J Klein-Seetharaman
    posted to folding helix membrane_proteins mutation rhodopsin structure transmembrane by xdeupi on 2007-06-25 10:08:49 as ** along with 1 group LabCompMed
  • Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting
    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
  • Combined solid state and solution NMR studies of alpha,epsilon-15N labeled bovine rhodopsin.
    J Biomol NMR, Vol. 37, No. 4. (April 2007), pp. 303-312.
    by K Werner, I Lehner, HK Dhiman, C Richter, C Glaubitz, H Schwalbe, J Klein-Seetharaman, HG Khorana
    posted to nmr rhodopsin structure by xdeupi on 2007-06-02 19:27:51 as ** along with 2 people and 1 group InesLehner netterpaladin LabCompMed
  • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    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.
    Curr Top Med Chem, Vol. 7, No. 10. (2007), pp. 999-1006.
    by X Deupi Nicole Dölker María Luz López-Rodríguez Mercedes Campillo Juan A Ballesteros And Leonardo Pardo, N Dölker, ML López-Rodríguez, M Campillo, JA 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
  • Computational prediction of atomic structures of helical membrane proteins aided by EM maps.
    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
  • Determining membrane protein structures: still a challenge!
    Trends Biochem Sci (2 May 2007)
    by Jean-Jacques J Lacapère, Eva Pebay-Peyroula, Jean-Michel M Neumann, Catherine Etchebest
    posted to dynamics membrane_proteins nmr review structure xray by xdeupi on 2007-05-15 12:52:21 as **** along with 1 person and 1 group gcaltabiano LabCompMed
  • Helix packing moments reveal diversity and conservation in membrane protein structure.
    J Mol Biol, Vol. 337, No. 3. (26 March 2004), pp. 713-729.
    by W Liu, M Eilers, AB Patel, SO Smith
    posted to gpcr helix membrane_proteins rhodopsin sequence ser structure transmembrane by xdeupi on 2007-04-26 13:49:38 as ***** along with 1 group LabCompMed
  • Peptide design and structural characterization of a GPCR loop mimetic.
    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.
    Annu Rev Pharmacol Toxicol, Vol. 47 (2007), pp. 53-87.
    by MJ Smit, HF Vischer, RA Bakker, 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
    Current Opinion in Structural Biology, 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 4 people and 1 group apaydin cactus biehl allmensch LabCompMed
  • Method To Assess Packing Quality of Transmembrane alpha-Helices in Proteins. 1. Parametrization Using Structural Data.
    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
  • Structure and conformational changes in the C-terminal domain of the beta 2-adrenoceptor: Insights from fluorescence resonance energy tranfer studies.
    J Biol Chem (8 March 2007)
    by Sebastien Granier, Samuel Kim, Aaron M M Shafer, 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
  • Discontinuous membrane helices in transport proteins and their correlation with function.
    J Struct Biol (1 February 2007)
    by Emanuela Screpanti, Carola Hunte
    posted to channel membrane_proteins structure transmembrane by xdeupi on 2007-03-21 11:35:11 as ** along with 1 person and 1 group Guff32 LabCompMed
  • Secondary structure, dynamics, and topology of a seven-helix receptor in native membranes, studied by solid-state NMR spectroscopy.
    Angew Chem Int Ed Engl, Vol. 46, No. 3. (2007), pp. 459-462.
    by M Etzkorn, S Martell, OC Andronesi, K Seidel, M Engelhard, M Baldus
    posted to membrane_proteins nmr structure by xdeupi on 2007-03-21 11:16:40 as ** along with 1 group LabCompMed
  • Two-dimensional solid-state NMR applied to a chimeric potassium channel.
    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
  • From Interactions of Single Transmembrane Helices to Folding of alpha-Helical Membrane Proteins: Analyzing Transmembrane Helix-Helix Interactions in Bacteria.
    Curr Protein Pept Sci, Vol. 8, No. 1. (February 20067), pp. 45-61.
    by Dirk Schneider, Carmen Finger, Alexander Prodöhl, Thomas Volkmer
    posted to helix membrane_proteins review sequence structure transmembrane by xdeupi on 2007-02-26 09:06:23 as ** along with 1 group LabCompMed
  • Progress in structure prediction of alpha-helical membrane proteins.
    Curr Opin Struct Biol (3 July 2006)
    by Sarel J J Fleishman, Nir Ben-Tal
    posted to helix membrane_proteins review structure transmembrane by xdeupi on 2007-02-13 15:11:51 as ***** along with 1 person and 1 group wouterboomsma LabCompMed
  • Membrane-protein topology
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 12., pp. 909-918.
    by Gunnar von Heijne
    posted to transmembrane structure review membrane_proteins lmc_101 genome by xdeupi on 2006-12-11 10:31:16 as ** along with 3 people and 3 groups dchughes nm merj G4ID LabCompMed Genetics-of-Gambling
  • G-protein coupled receptor structure.
    Biochim Biophys Acta (10 October 2006)
    by Philip L L Yeagle, Arlene D D Albert
    posted to activation gpcr review rhodopsin structure by xdeupi on 2006-11-17 20:57:15 as ***** along with 4 people and 1 group gcaltabiano merj superpyrin adamsdi LabCompMed
  • Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer.
    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.
    Biophys J, Vol. 91, No. 7. (1 October 2006), pp. 2647-2664.
    by C Beier, HJ 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
    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 no-tag npxxy nterm opioid pharmacology polymorphism pro-kink protonation review rhodopsin s542 sequence ser spin_labeling structure switch test 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
  • Local peptide movement in the photoreaction intermediate of rhodopsin.
    Proc Natl Acad Sci U S A, Vol. 103, No. 34. (22 August 2006), pp. 12729-12734.
    by H Nakamichi, T Okada
    posted to activation crystallography retinal rhodopsin structure by xdeupi on 2006-10-26 11:39:03 as ** along with 1 group LabCompMed
  • Crystallographic analysis of primary visual photochemistry.
    Angew Chem Int Ed Engl, Vol. 45, No. 26. (26 June 2006), pp. 4270-4273.
    by H Nakamichi, T Okada
    posted to activation crystallography rhodopsin structure by xdeupi on 2006-10-26 11:36:51 as ** along with 1 group LabCompMed
  • Crystal structure of a photoactivated deprotonated intermediate of rhodopsin.
    Proc Natl Acad Sci U S A (23 October 2006)
    by David Salom, David T T Lodowski, Ronald E E Stenkamp, Isolde Le Trong, Marcin Golczak, Beata Jastrzebska, Tim Harris, Juan A A Ballesteros, Krzysztof Palczewski
    posted to activation crystallography dimer rhodopsin structure by xdeupi on 2006-10-26 09:58:37 as read along with 1 person and 1 group cen4ik LabCompMed
  • Helix-packing motifs in membrane proteins.
    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
  • Mutational and bioinformatics analysis of proline- and glycine-rich motifs in vesicular acetylcholine transporter
    Journal of Neurochemistry, Vol. 98, No. 5. (September 2006), pp. 1551-1559.
    by Chandrasekaran, Ananda, Ojeda, M Ana, Kolmakova, G Natalia, Parsons, M Stanley
    posted to activation channel gly helix mutation pro-kink structure transmembrane by xdeupi on 2006-09-05 11:43:55 as ** along with 1 group LabCompMed
  • Asymmetric stability among the transmembrane helices of lactose permease.
    Biochemistry, Vol. 45, No. 26. (4 July 2006), pp. 8088-8095.
    by M Bennett, R D'Rozario, MS Sansom, PL 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.
    J Biol Chem, Vol. 281, No. 26. (30 June 2006), pp. 18120-18125.
    by B Behr, C Hoffmann, G Ottolina, KN 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
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