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dimkas library [549 articles]

Senaste artiklarna i dimkas bibliotek.
  • Conformational Changes and Gating at the Selectivity Filter of Potassium Channels
    J. Am. Chem. Soc. (28 June 2008)
    by Carmen Domene, Michael L Klein, Davide Branduardi, Francesco L Gervasio, Michele Parrinello
    posted to simulation selectivity md lipids kirbac by dimka on 2008-07-01 00:10:09 as **
  • Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions
    J. Phys. Chem. B, Vol. 108, No. 14. (8 April 2004), pp. 4485-4494.
    by M Patra, M Karttunen, MT Hyvonen, E Falck, I Vattulainen
    posted to simulations md gromacs dppc by dimka on 2008-06-27 04:38:49 as ** along with 1 person softsimu
  • Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers
    European Biophysics Journal, Vol. 37, No. 2. (11 February 2008), pp. 131-141.
    by Katherine Cox, Peter Bond, Alessandro Grottesi, Marc Baaden, Mark Sansom
    posted to simulation protein membrane md compare by dimka on 2008-06-25 16:48:52 as **
  • Anisotropic network model: systematic evaluation and a new web interface
    Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2619-2627.
    by Eyal, Eran, Yang, Lee-Wei, Bahar, Ivet
    posted to protein motion enm elastic by dimka on 2008-06-10 19:49:58 as ** along with 1 person aqeel
  • Electrostatic Complementarity at Ligand Binding Sites: Application to Chorismate Mutase
    J. Phys. Chem. B, Vol. 105, No. 4. (1 February 2001), pp. 880-888.
    by E Kangas, B Tidor
    posted to electrostatics by dimka on 2008-06-04 00:53:51 as **
  • Structural Insight into Epitopes in the Pregnancy-Associated Malaria Protein VAR2CSA
    PLoS Pathog, Vol. 4, No. 2. (Feb 2008)
    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 2008-05-29 20:16:55 as **
  • Interactions of the Pleckstrin Homology Domain with Phosphatidylinositol Phosphate and Membranes: Characterization via Molecular Dynamics Simulations
    Biochemistry (15 March 2008)
    by Emi Psachoulia, Mark S Sansom
    posted to simulations protein-membrane protein-lipid protein-ligand phosphoinositides md inositiol by dimka on 2008-05-28 22:02:54 as ** along with 2 people choonpeng paulschlesinger
  • Synthesis and biological activity of phosphatidylinositol-3,4,5-trisphosphorothioate
    Bioorganic & Medicinal Chemistry Letters, Vol. 18, No. 2. (15 January 2008), pp. 762-766.
    by Honglu Zhang, Yong Xu, Nicolas Markadieu, Renaud Beauwens, Christophe Erneux, Glenn D Prestwich
    posted to synthesis pip3 pip2 phosphoinositides by dimka on 2008-05-28 19:34:13 as **
  • Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation.
    The Journal of chemical physics, Vol. 128, No. 19. (21 May 2008)
    by Nobuyuki Matubayasi, Wataru Shinoda, Masaru Nakahara
    posted to membrane lipids free-energy deltag by dimka on 2008-05-27 23:04:38 as **
  • The "Electrostatic-Switch" Mechanism: Monte Carlo Study of MARCKS-Membrane Interaction
    Biophys. J. (23 May 2008), biophysj.108.132522.
    by Shelly Tzlil, Diana Murray, Avinoam Ben-Shaul
    posted to pip2 marcks electrostatics by dimka on 2008-05-27 23:00:21 as ** along with 1 person paulschlesinger
  • Giant unilamellar vesicles containing phosphatidylinositol(4,5)bisphosphate : characterization and functionality
    Biophys. J. (23 May 2008), biophysj.107.126912.
    by Kevin Carvalho, Laurence Ramos, Christian Roy, Catherine Picart
    posted to sequestering pip2 by dimka on 2008-05-27 22:52:03 as ** along with 1 person paulschlesinger
  • A structural link between inactivation and block of a K(+) channel.
    Nature structural & molecular biology (18 May 2008)
    by Christian Ader, Robert Schneider, Sönke Hornig, Phanindra Velisetty, Erica M M Wilson, Adam Lange, Karin Giller, Iris Ohmert, Marie-France F Martin-Eauclaire, Dirk Trauner, Stefan Becker, Olaf Pongs, Marc Baldus
    posted to ph kv13 kir kcsa gating blocker by dimka on 2008-05-22 15:50:21 as ** along with 1 person paulschlesinger
  • A heuristic procedure for the detection of locally similar substructures of two equivalent structures.
    Protein Eng, Vol. 7, No. 3. (March 1994), pp. 331-333.
    by M Mezei
    posted to md-analysis hinge by dimka on 2008-05-14 19:31:51 as ** along with 1 person ttjoseph
  • Generic Solvation Sites in a Crystal
    J. Comp. Chem., Vol. 6 (1984), pp. 523-527.
    by M Mezei, DL Beveridge
    posted to simulaid rdf md-analysis density by dimka on 2008-05-14 18:36:33 as **
  • Essential dynamics of proteins.
    Proteins, Vol. 17, No. 4. (December 1993), pp. 412-425.
    by A Amadei, AB Linssen, HJ Berendsen
    posted to simulations pca md-analysis md dynamics by dimka on 2008-05-14 01:42:48 as ** along with 7 people and 1 group baaden aqeel yongzhao ttjoseph ffranca allmensch carlescorbi TSRI_MGL
  • Simulaid
    http://atlas.physbio.mssm.edu/~mezei/simulaid/
    by Mihaly Mezei
    posted to simulaid md-analysis md analysis by dimka on 2008-05-14 01:35:17 as **
  • Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating.
    Biophysical journal, Vol. 88, No. 5. (May 2005), pp. 3310-3320.
    by S Haider, A Grottesi, BA Hall, FM Ashcroft, MS Sansom
    posted to simulations md kir katp by dimka on 2008-05-14 00:48:45 as ** along with 1 person mengcite
  • Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by 2H NMR Spectroscopy
    Biophys. J., Vol. 79, No. 6. (1 December 2000), pp. 3172-3192.
    by Horia I Petrache, Steven W Dodd, Michael F Brown
    posted to nmr lipid-area lipid area by dimka on 2008-05-13 22:16:55 as **
  • Molecular areas of phospholipids as determined by 2H NMR spectroscopy. Comparison of phosphatidylethanolamines and phosphatidylcholines.
    Biophys. J., Vol. 59, No. 1. (1 January 1991), pp. 108-113.
    by RL Thurmond, SW Dodd, MF Brown
    posted to scd lipid-order-parameter experimental dppc by dimka on 2008-05-13 22:09:29 as **
  • Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study
    Biophys. J., Vol. 88, No. 6. (1 June 2005), pp. 3822-3828.
    by Steve O Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B Moore, Michael L Klein
    posted to simulation perturbation nanotube md lipid by dimka on 2008-05-13 21:14:16 as ** along with 1 person loison
  • The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations.
    J Phys Chem B (15 June 2007)
    by Siewert J Marrink, H J Risselada, Serge Yefimov, D P Tieleman, Alex H Vries
    posted to simulations md force-field coarse-grain by dimka on 2008-05-13 21:10:45 as ** along with 2 people choonpeng softsimu
  • Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ninad V Prabhu, Manoranjan Panda, Qingyi Yang, Kim A Sharp
    posted to simulations md implicit-water charged by dimka on 2008-05-13 21:00:30 as ** along with 3 people and 1 group sobolevnrm RamuAnandakrishnan onufriev baker-group
  • An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins.
    Biophysical journal, Vol. 85, No. 5. (November 2003), pp. 2900-2918.
    by W Im, M Feig, CL Brooks
    posted to model membrane implicit-membrane implicit by dimka on 2008-05-13 20:56:12 as **
  • Molecular mechanism of pH sensing in KcsA potassium channels
    Proceedings of the National Academy of Sciences, Vol. 105, No. 19. (13 May 2008), pp. 6900-6905.
    by Ameer N Thompson, David J Posson, Pirooz V Parsa, Crina M Nimigean
    posted to ph-sensor open-closed mthk kcsa by dimka on 2008-05-13 20:03:33 as **
  • Protein interaction property similarity analysis
    International Journal of Quantum Chemistry, Vol. 83, No. 3-4. (26 April 2001), pp. 122-127.
    by RC Wade, RR Gabdoulline, F De Rienzo
    posted to protein-ligand interaction electrostatic compare by dimka on 2008-05-12 21:48:40 as **
  • Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects
    Journal of Computer-Aided Molecular Design, Vol. 8, No. 5. (1 October 1994), pp. 513-525.
    by Chau, PM Dean
    posted to ligand electrostatic-complementarity electrostatic drug-design by dimka on 2008-05-12 21:31:48 as **
  • Spatial distribution functions as a tool in the analysis of ribonucleic acids hydration -- molecular dynamics studies
    Computers & Chemistry, Vol. 24, No. 3-4. (May 2000), pp. 451-457.
    by K Kulinska, T Kulinski, A Lyubartsev, A Laaksonen, RW Adamiak
    posted to sdf rdf organization distribution by dimka on 2008-05-12 19:15:25 as **
  • Microscopic theory of the dielectric properties of proteins.
    Biophysical journal, Vol. 59, No. 3. (March 1991), pp. 670-690.
    by T Simonson, D Perahia, AT Brünger
    posted to electrostatics dielectric by dimka on 2008-05-12 18:21:33 as **
  • Dielectric relaxation in proteins: the computational perspective.
    Photosynthesis research (29 April 2008), pp. 0166-8595.
    by Thomas Simonson
    posted to electrostatics dielectric by dimka on 2008-05-12 18:20:27 as **
  • Tanford-Kirkwood electrostatics for protein modeling.
    Proc Natl Acad Sci U S A, Vol. 96, No. 20. (28 September 1999), pp. 11145-11150.
    by JJ Havranek, PB Harbury
    posted to electrostatics by dimka on 2008-05-12 18:14:42 as ** along with 1 person onufriev
  • Focus on Kir6.2: a key component of the ATP-sensitive potassium channel.
    Journal of molecular and cellular cardiology, Vol. 38, No. 6. (June 2005), pp. 927-936.
    by S Haider, JF Antcliff, P Proks, MS Sansom, FM Ashcroft
    posted to simulation md kir62 katp atp by dimka on 2008-05-09 21:33:30 as **
  • PIP2 and PIP as Determinants for ATP Inhibition of KATP Channels
    Science, Vol. 282, No. 5391. (6 November 1998), pp. 1141-1144.
    by Thomas Baukrowitz, Uwe Schulte, Dominik Oliver, Stefan Herlitze, Tobias Krauter, Stephen J Tucker, Peter J Ruppersberg, Bernd Fakler
    posted to pip2 phosphoinositides kir62 katp atp by dimka on 2008-05-09 21:28:51 as **
  • Homology Modeling and Molecular Dynamics Simulation Studies of an Inward Rectifier Potassium Channel
    Biophys. J., Vol. 78, No. 6. (1 June 2000), pp. 2929-2942.
    by Charlotte E Capener, Indira H Shrivastava, Kishani M Ranatunga, Lucy R Forrest, Graham R Smith, Mark S Sansom
    posted to tertiapin simulation kir kcsa by dimka on 2008-05-09 20:40:16 as **
  • Effect of Ions on a Dipalmitoyl Phosphatidylcholine Bilayer. A Molecular Dynamics Simulation Study
    J. Phys. Chem. B (15 January 2008)
    by A Cordomi, O Edholm, JJ Perez
    posted to simulation lipid-area lipid dppc by dimka on 2008-05-08 23:58:41 as ** along with 2 people and 1 group sobolevnrm softsimu baker-group
  • Molecular dynamics simulations of potassium channels
    Central European Journal of Chemistry, Vol. 5, No. 3. (2007), pp. 635-671.
    by Carmen Domene
    posted to simulation review md kir channels by dimka on 2008-05-08 23:28:34 as **
  • What is principal component analysis?
    Nature Biotechnology, Vol. 26, No. 3. (2008), pp. 303-304.
    by Markus Ringnér
    posted to review pca by dimka on 2008-05-08 23:06:54 as ** along with 48 people and 3 groups tharris rsantana kengg laharrin chrissp100 xingxu dekay23 rvosa i-stevenson dayjm markusd ashko craigwilson06 abbie_riner quianominorleo bibay2004 jfr kristgy pavanghatty rchauhan waghsk hpaces adacier fryanpan sobolevnrm Yanno jyuh operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu FAB-lab Bioinformatics baker-group
  • Sodium Coordination Site Reveals a Novel Sodium-Sensitive Phenotype in Kir Channels
    In Preparation (2008)
    by Avia Rosenhouse-Dantsker, Jun L Sui, Qu Zhao, Radda Rusinova, Diomedes E Logothetis
    posted to sodium md kir by dimka on 2008-05-08 16:56:32 as **
  • Polyphosphoinositides undergo charge neutralization in the physiological pH range: a 31P-NMR study.
    Biochimica et biophysica acta, Vol. 877, No. 1. (11 June 1986), pp. 216-219.
    by PA van Paridon, B de Kruijff, R Ouwerkerk, KW Wirtz
    posted to protonation pip2 nmr charge by dimka on 2008-05-07 21:21:36 as **
  • RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes
    Nucl. Acids Res. (6 May 2008), gkn197.
    by Roberto Mosca, Thomas R Schneider
    posted to mmult-ref by dimka on 2008-05-07 19:42:39 as **
  • Biological Membranes: A Molecular Perspective from Computation and Experiment
    (30 July 1996)
    by Kenneth Merz, Benoit Roux
    posted to simulation membrane lipid by dimka on 2008-05-07 07:29:15 as **
  • Stoichiometry of Kir channels with phosphatidylinositol bisphosphate
    Channels, Vol. 2, No. 1. (January 2008)
    by Taihao Jin, Jin L Sui, Avia Rosenhouse-Dantsker, Kim Chan, Lily Jan, Diomedes E Logothetis
    edited by Gerald Zamponi
    posted to stoichiometry pip2 phosphoinositides kir34 kir21 by dimka on 2008-05-07 03:16:24 as **
  • Structural Diversity in the Cytoplasmic Region of G Protein-Gated Inward Rectifier K+ Channels
    Channels, Vol. 1, No. 1. (January 2007), pp. 39-45.
    by Atsushi Inanobe, Takanori Matsuura, Atsushi Nakagawa, Yoshihisa Kurachi
    edited by Gerald Zamponi
    posted to structure kir32 girk2 by dimka on 2008-05-06 21:54:18 as **
  • Statistical potential for assessment and prediction of protein structures.
    Protein Sci, Vol. 15, No. 11. (November 2006), pp. 2507-2524.
    by MY Shen, A Sali
    posted to modeller dope_score by dimka on 2008-05-03 04:31:26 as ** along with 3 people wouterboomsma j3xucite cdeane
  • Advances in comparative protein-structure modelling.
    Current opinion in structural biology, Vol. 7, No. 2. (April 1997), pp. 206-214.
    by R Sánchez, A Sali
    posted to modeller by dimka on 2008-05-03 04:28:21 as **
  • Mutations in the ROMK gene in antenatal Bartter syndrome are associated with impaired K+ channel function.
    Biochemical and biophysical research communications, Vol. 230, No. 3. (23 January 1997), pp. 641-645.
    by C Derst, M Konrad, A Köckerling, L Károlyi, G Deschenes, J Daut, A Karschin, HW Seyberth
    posted to romk kir11 bartter by dimka on 2008-05-03 04:02:48 as **
  • Characteristic microscopic interaction kinetics of K+ channels with either Gβγ or PIP2 implicate control of distinct gating structures.
    In Preparation
    by Taihao Jin, Bensheng Liu, Radda Rusinova, Matthew G Hopperstad, Diomedes E Logothetis
    posted to single-channel selectivity pip2 kir34 kir31 girk4 girk1 gating by dimka on 2008-05-03 00:12:29 as **
  • Phosphoinositide profiling in complex lipid mixtures using electrospray ionization mass spectrometry.
    Nature biotechnology, Vol. 21, No. 7. (July 2003), pp. 813-817.
    by MR Wenk, L Lucast, G Di Paolo, AJ Romanelli, SF Suchy, RL Nussbaum, GW Cline, GI Shulman, W McMurray, P De Camilli
    posted to pis pi phosphoinositides abundance by dimka on 2008-05-02 06:57:25 as **
  • Phosphoinositide signaling disorders in human diseases.
    FEBS letters, Vol. 546, No. 1. (3 July 2003), pp. 25-31.
    by C Pendaries, H Tronchère, M Plantavid, B Payrastre
    posted to phosphinositides disease by dimka on 2008-05-02 06:13:32 as **
  • Molecular dynamics simulations of membrane proteins.
    Methods in molecular biology (Clifton, N.J.), Vol. 443 (2008), pp. 147-160.
    by PC Biggin, PJ Bond
    posted to simulations review membrane-protein md by dimka on 2008-05-01 15:18:37 as **
  • Implicit membrane models for membrane protein simulation.
    Methods in molecular biology (Clifton, N.J.), Vol. 443 (2008), pp. 181-196.
    by M Feig
    posted to review membrane implicit-membrane implicit by dimka on 2008-05-01 15:17:44 as **
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