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dimka's library [568 articles]

最近录入 dimka's ordered by to_read.
  • Ion Conduction through MscS as Determined by Electrophysiology and Simulation.
    Biophys J (17 November 2006)
    by Marcos Sotomayor, Valeria Vasquez, Eduardo Perozo, Klaus Schulten
    posted to channel lipid membrane mscs simulation by dimka on 2006-11-28 20:25:33 as *****
  • Lipid bilayer pressure profiles and mechanosensitive channel gating.
    Biophys J, Vol. 86, No. 6. (June 2004), pp. 3496-3509.
    by J Gullingsrud, K Schulten
    posted to channel gating lipid-area mechanosensitive mscl order-parameter by dimka on 2005-11-16 20:17:01 as ***** along with 1 person viktor21614
  • Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation.
    Science, Vol. 314, No. 5801. (10 November 2006), pp. 1004-1007.
    by FI Valiyaveetil, M Leonetti, TW Muir, R Mackinnon
    posted to channel kcsa kir open selectivity by dimka on 2006-11-16 16:05:19 as ****
  • A novel KCNJ11 mutation associated with congenital hyperinsulinism reduces the intrinsic open probability of beta-cell ATP-sensitive potassium channels.
    J Biol Chem, Vol. 281, No. 5. (3 February 2006), pp. 3006-3012.
    by YW Lin, C MacMullen, A Ganguly, CA Stanley, SL Shyng
    posted to atp katp kir kir62 mutation pip2 by dimka on 2006-05-11 23:02:59 as ****
  • Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion.
    Methods Enzymol, Vol. 127 (1986), pp. 21-47.
    by M Mezei, DL Beveridge
    posted to mc mmc proximity-analysis qcdf rdf by dimka on 2006-04-20 17:08:47 as ****
  • Detailed microscopic study of the full zipA:FtsZ interface.
    Proteins (14 March 2006)
    by I S S Moreira, P A A Fernandes, M J J Ramos
    posted to ala-scanning irina by dimka on 2006-03-23 03:44:51 as **** along with 1 person IrinaMoreira
  • Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis.
    Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 994-999.
    by RA Estabrook, J Luo, MM Purdy, V Sharma, P Weakliem, TC Bruice, NO Reich
    posted to analysis coevolutionary covariance sca statistical by dimka on 2006-03-21 04:59:51 as **** along with 4 people and 2 groups ana barry pansapiens gbart structural_bioinformatics Bioinformatics
  • Hydrogen bonding dynamics between adjacent blades in G protein beta subunit regulate GIRK channel activation.
    Biophys J (20 January 2006)
    by Tooraj Mirshahi, Diomedes E E Logothetis, Avia Rosenhouse-Dantsker
    posted to g-protein girk by dimka on 2006-03-20 17:39:50 as ****
  • Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 1. (12 January 2006), pp. 548-556.
    by S Tanizaki, M Feig
    posted to gb implicit md membrane protein water by dimka on 2006-03-06 16:15:20 as **** along with 2 people and 1 group onufriev xdeupi LabCompMed
  • Model of an asymmetric DPPC/DPPS membrane: effect of asymmetry on the lipid properties. A molecular dynamics simulation study.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 5. (9 February 2006), pp. 2358-2363.
    by JJ López Cascales, TF Otero, BD Smith, C González, M Márquez
    posted to dppc dpps lipid membrane by dimka on 2006-03-06 16:10:53 as ****
  • Multiple Alignment of protein structures and sequences for VMD
    Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 504-506.
    by John Eargle, Dan Wright, Zaida Luthey-Schulten
    posted to alignment multiple protein structure by dimka on 2006-02-18 00:24:50 as **** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • GROMACS: fast, flexible, and free.
    J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1701-1718.
    by D van der Spoel, E Lindahl, B Hess, G Groenhof, AE Mark, HJ Berendsen
    posted to dynamics gromacs md molecular simulations by dimka on 2005-12-15 21:09:26 as **** along with 13 people and 2 groups sebk jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
  • One channel: open and closed.
    Structure (Camb), Vol. 13, No. 10. (October 2005), pp. 1398-1400.
    by JL Robertson, B Roux
    posted to close conformation cryomicroscopy electron kirbac31 open by dimka on 2005-10-23 23:03:55 as ****
  • Ligand binding affinities from MD simulations.
    Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 358-365.
    by J Aqvist, VB Luzhkov, BO Brandsdal
    posted to lie linear-energy-interaction md by dimka on 2005-09-30 22:09:29 as **** along with 3 people and 2 groups barry baaden superpyrin structural_bioinformatics Bioinformatics
  • The linear interaction energy method for predicting ligand binding free energies.
    Comb Chem High Throughput Screen, Vol. 4, No. 8. (December 2001), pp. 613-626.
    by J Aqvist, J Marelius
    posted to lie linear-energy-interaction theory by dimka on 2005-09-30 22:07:02 as **** along with 1 person baaden
  • Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.
    Biophys J, Vol. 84, No. 6. (June 2003), pp. 3636-3645.
    by M Patra, M Karttunen, MT Hyvönen, E Falck, P Lindqvist, I Vattulainen
    posted to dppc dynamics lipid-area membrane molecular by dimka on 2005-09-20 22:26:26 as **** along with 2 people easybakemuffin softsimu
  • Mechanism of rectification in inward-rectifier K+ channels.
    Annu Rev Physiol, Vol. 66 (2004), pp. 103-129.
    by Z Lu
    posted to channel mechanism rectification review by dimka on 2005-09-19 18:30:42 as **** along with 1 person batallah
  • Membrane protein structure quality in molecular dynamics simulation.
    J Mol Graph Model (12 August 2005)
    by Richard J J Law, Charlotte Capener, Marc Baaden, Peter J J Bond, Jeff Campbell, George Patargias, Yalini Arinaminpathy, Mark S P S Sansom
    posted to membrane protein review simulations by dimka on 2005-08-31 17:46:10 as **** along with 1 person baaden
  • A phosphorylation-dependent export structure in ROMK (KIR 1.1) channel overides an ER- localization signal.
    J Biol Chem (23 August 2005)
    by Dana Yoo, Liang Fang, Amanda Mason, Bo-Young Y Kim, Paul A A Welling
    posted to kir11 romk by dimka on 2005-08-27 08:44:19 as **** along with 1 person jenni_p
  • Multiple PIP2 binding sites in Kir2.1 inwardly rectifying potassium channels
    FEBS letters, Vol. 490, No. 1-2. (9 February 2001), pp. 49-53.
    by M Soom, R Schonherr, Y Kubo, C Kirsch, R Klinger, SH Heinemann
    posted to channel dose-response glutathione liposomes mutation relationship site-directed structure tertiary transcription transferase by dimka on 2005-06-06 17:48:04 as ****
  • Merging functional studies with structures of inward-rectifier K(+) channels
    Nature reviews. Neuroscience, Vol. 4, No. 12. (2003), pp. 957-967.
    by D Bichet, FA Haass, LY Jan
    posted to channel cytoplasm gating human inwardly ion molecular permeability potassium rectifying relationship structure structure-activity by dimka on 2005-06-06 17:47:38 as ****
  • MD simulation of asymmetric phospholipid bilayers with ions and cholesterols
    Chem-Bio Informatics Journal, Vol. 4, No. 1. (2004), pp. 15-26.
    by Kenichi Mori, Masayuki Hata, Saburo Neya, Tyuji Hoshino
    posted to asymmetry bilayer chlesterol lipids md popc pope pops by dimka on 2006-12-10 23:36:30 as ***
  • A novel fingerprint for the characterization of protein folds.
    Protein Eng, Vol. 16, No. 10. (October 2003), pp. 713-715.
    by M Mezei
    posted to classification domain fingerprint by dimka on 2006-06-15 19:18:11 as ***
  • Graph Clustering and Minimum Cut Trees
    Internet Math, Vol. 1, No. 4. (2003), pp. 385-408.
    by Gary W Flake, Robert E Tarjan, Kostas Tsioutsiouliklis
    posted to culstering graph tree by dimka on 2006-06-13 19:54:26 as ***
  • Molecular Dynamics study of MscL interactions with a curved lipid bilayer.
    Biophys J (2 June 2006)
    by Grischa R R Meyer, Justin Gullingsrud, Klaus Schulten, Boris Martinac
    posted to lipids md mechanosensitive membrane mscl simulation by dimka on 2006-06-09 18:38:04 as ***
  • Molecular dynamics simulations of unsaturated lipid bilayers: effects of varying the numbers of double bonds.
    Eur Biophys J, Vol. 34, No. 4. (June 2005), pp. 294-305.
    by MT Hyvönen, PT Kovanen
    posted to double-bond lipid md unsaturated by dimka on 2006-04-07 22:10:49 as *** along with 1 person softsimu
  • Interaction between K(+) channel gate modifier hanatoxin and lipid bilayer membranes analyzed by molecular dynamics simulation.
    Eur Biophys J, Vol. 35, No. 5. (2 May 2006), pp. 373-381.
    by Manami Nishizawa, Kazuhisa Nishizawa
    posted to kv lipid-protein md simulation structural-modelling by dimka on 2006-02-07 18:23:58 as ***
  • Energetics of ion conduction through the K+ channel.
    Nature, Vol. 414, No. 6859. (1 November 2001), pp. 73-77.
    by S Bernèche, B Roux
    posted to conductivity ion kcsa kir permeation by dimka on 2005-12-26 07:49:28 as *** along with 1 person and 1 group brocktice TulaneCEP
  • Molecular dynamics simulation of a phosphatidylglycerol membrane.
    FEBS Lett (6 December 2005)
    by Donald E E Elmore
    posted to bilayer lipid popc popg properties simulations by dimka on 2005-12-25 22:17:34 as *** along with 3 people and 4 groups piscinero xdeupi softsimu Fluid-Mechanics-and-Thermal-Science-Research Computational_Systems_Biology XMLDataManagement LabCompMed
  • A New Technique for Finding Needles in Haystacks: A Geometric Approach to Distinguishing Between a New Source and Random Fluctuations
    ArXiv Physics e-prints (May 2005)
    by RS Pilla, C Loader, C Taylor
    posted to montecarlo noise signal significance statistice by dimka on 2005-12-07 21:09:40 as ***
  • Role of Aromatic Localisation in the Gating Process of a Potassium Channel.
    Biophys J (16 September 2005)
    by Carmen Domene, Satyavani Vemparala, Michael L L Klein, Catherine Venien-Brian, Declan A A Doyle
    posted to kirbac11 by dimka on 2005-09-26 19:20:21 as ***
  • PIP2 signaling in lipid domains: a critical re-evaluation
    The EMBO Journal, Vol. aop, No. current. (21 April 2005)
    by Jacco v van Rheenen, Eskeatnaf M Achame, Hans Janssen, Jero Calafat, Kees Jalink
    posted to lipid pip2 by dimka on 2005-09-23 20:57:44 as ***
  • PIP2 hydrolysis underlies agonist-induced inhibition and regulates voltage gating of two-pore domain K+ channels
    The Journal of Physiology, Vol. 564, No. 1. (April 2005), pp. 117-129.
    by MB Lopes, Rohacs Tibor, Czirjak Gabor, Balla Tamas, Enyedi Peter, E Logothetis
    posted to gating hydrolysis k-channel pip2 two-pore by dimka on 2005-09-19 22:16:07 as ***
  • Modeling ion channel regulation
    Current Opinion in Chemical Biology, Vol. 7, No. 6. (December 2003), pp. 710-714.
    by GA Woolley, T Lougheed
    posted to gating ligand-gated mechanosensitive models proton review voltage-gated by dimka on 2005-09-01 16:11:51 as ***
  • Crystal structure of a mammalian voltage-dependent Shaker family K+ channel.
    Science, Vol. 309, No. 5736. (5 August 2005), pp. 897-903.
    by SB Long, EB Campbell, R Mackinnon
    posted to channel kir kv12 open structure by dimka on 2005-08-30 16:41:09 as *** along with 2 people baniel davidcsterratt
  • Differential distribution of individual subunits of strongly inwardly rectifying potassium channels (Kir2 family) in rat brain.
    Brain Res Mol Brain Res (2 June 2005)
    by Harald Prüss, Christian Derst, Reinhard Lommel, Rüdiger W W Veh
    posted to channel irk kir2 rats subunit by dimka on 2005-08-27 08:46:37 as ***
  • Performance of the general amber force field in modeling aqueous POPC membrane bilayers.
    J Comput Chem, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058.
    by Balázs Jójárt, Tamás A A Martinek
    posted to simulation membrane md lipid amber by dimka on 2008-11-11 21:48:17 as ** along with 3 people and 1 group xdeupi easybakemuffin viktor21614 LabCompMed
  • The molecular face of lipid rafts in model membranes
    Proceedings of the National Academy of Sciences (5 November 2008)
    by Jelger H Risselada, Siewert J Marrink
    posted to simulations mixture md lipids by dimka on 2008-11-07 20:27:12 as ** along with 6 people and 2 groups wsjames reister paulschlesinger chiufanlee barry kshundyak Oxford Virology McCammon
  • Hydration forces between phospholipid bilayers
    Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, Vol. 988, No. 3. (6 December 1989), pp. 351-376.
    by RP Rand, VA Parsegian
    posted to simulation review membrane md lipid equilibration by dimka on 2008-10-29 00:10:07 as ** along with 1 person softsimu
  • Alignment of protein structures in the presence of domain motions
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Roberto Mosca, Barbara Brannetti, Thomas Schneider
    posted to structure mmult-ref by dimka on 2008-10-21 19:13:21 as ** along with 4 people viktor21614 neils reyez vinithepooh
  • Dynamic control of slow water transport by aquaporin 0: Implications for hydration and junction stability in the eye lens
    Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (2008), pp. 14430-14435.
    by Morten Jensen, Ron O Dror, Huafeng Xu, David W Borhani, Isaiah T Arkin, Michael P Eastwood, David E Shaw
    posted to md desmond aquaporin by dimka on 2008-10-16 18:43:08 as ** along with 1 person agrossfield
  • Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers
    Biophys. J. (3 October 2008), biophysj.108.138677.
    by Beate West, Frank L Brown, Friederike Schmid
    posted to membrane-protein med mc coarse-grain by dimka on 2008-10-07 19:20:34 as ** along with 1 person paulschlesinger
  • GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences.
    Methods in enzymology, Vol. 374 (2003), pp. 492-509.
    by D Petrey, B Honig
    posted to poisson-bolzmann pb grasp electrostatic by dimka on 2008-10-02 07:01:00 as **
  • Determination of component volumes of lipid bilayers from simulations.
    Biophysical journal, Vol. 72, No. 5. (May 1997), pp. 2237-2242.
    by HI Petrache, SE Feller, JF Nagle
    posted to volume simulations methods md lipid dppc by dimka on 2008-09-25 21:02:11 as **
  • Dissection of the components for PIP2 activation and thermosensation in TRP channels
    Proceedings of the National Academy of Sciences, Vol. 104, No. 24. (12 June 2007), pp. 10246-10251.
    by Sebastian Brauchi, Gerardo Orta, Carolina Mascayano, Marcelo Salazar, Natalia Raddatz, Hector Urbina, Eduardo Rosenmann, Fernando Gonzalez-Nilo, Ramon Latorre
    posted to trp8 trp structure pip2 modeling channel by dimka on 2008-09-24 05:14:42 as **
  • The Use of a Conformational Alphabet for Fast Alignment of Protein Structures
    Bioinformatics Research and Applications (2008), pp. 331-342.
    by Wei-Mou Zheng
    posted to mmult-ref by dimka on 2008-09-18 17:02:29 as **
  • Structural Insight into Epitopes in the Pregnancy-Associated Malaria Protein VAR2CSA
    PLoS Pathog, Vol. 4, No. 2. (15 February 2008), e42.
    by Pernille Andersen, Morten A Nielsen, Mafalda Resende, Thomas S Rask, Madeleine Dahlbäck, Thor Theander, Ole Lund, Ali Salanti
    posted to mmult-ref by dimka on 2008-09-18 16:57:21 as **
  • A sodium-mediated structural switch that controls the sensitivity of Kir channels to PtdIns(4,5)P(2).
    Nature chemical biology (14 September 2008)
    by Avia Rosenhouse-Dantsker, Jin L L Sui, Qi Zhao, Radda Rusinova, Aldo A A Rodríguez-Menchaca, Zhe Zhang, Diomedes E E Logothetis
    posted to sodium pip2 md kir by dimka on 2008-09-17 17:49:36 as **
  • A molecular dynamics approach to study the importance of solvent in protein interactions
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Sergey Samsonov, Joan Teyra, Teresa M Pisabarro
    posted to mmult-ref by dimka on 2008-08-27 14:20:30 as ** along with 2 people jteyra Lombardo_7
  • Local interactions in protein folding determined through an inverse folding model.
    Proteins, Vol. 71, No. 1. (April 2008), pp. 278-299.
    by U Bastolla, M Porto, AR Ortíz
    posted to mmult-ref by dimka on 2008-08-25 21:52:26 as **
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