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dimka's library [572 articles]

Recent papers added to dimka's library.
  • 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 **
  • Molecular dynamics study of interaction of dimyristoyl phosphotidyl choline with water.
    Journal of Biosciences, Vol. 21, No. 5. (September 1996), pp. 577-597.
    by V Kothekar
    posted to no-tag by dimka on 2008-08-20 19:39:35 as **
  • Molecular dynamics simulation of hydrated phospholipid bilayers.
    Indian journal of biochemistry & biophysics, Vol. 33, No. 6. (December 1996), pp. 431-447.
    by V Kothekar
    posted to dmpc lipid md membrane simulation by dimka on 2008-08-20 19:33:30 as **
  • Cholesterol Packing around Lipids with Saturated and Unsaturated Chains: A Simulation Study
    Langmuir (3 June 2008)
    by Sagar A Pandit, See-Wing Chiu, Eric Jakobsson, Ananth Grama, HL Scott
    posted to cholesterol dopc md simulation by dimka on 2008-08-18 22:53:18 as ** along with 2 people and 1 group paulschlesinger sobolevnrm baker-group
  • Structural Information and Hidden Markov Models for Biological Sequence Analysis
    by Jeanette Tangrot
    posted to mmult-ref by dimka on 2008-08-18 22:03:24 as **
  • How Highly Charged Anionic Lipids Bind and Regulate Ion Channels
    J. Gen. Physiol., Vol. 131, No. 5. (28 April 2008), pp. 431-438.
    by Stephen J Tucker, Thomas Baukrowitz
    posted to katp kir62 modeling pip2 review by dimka on 2008-08-08 16:13:08 as **
  • Inward Rectifier Potassium Currents as a Target for Atrial Fibrillation Therapy.
    Journal of cardiovascular pharmacology (29 July 2008)
    by Joachim R Ehrlich
    posted to desease kir by dimka on 2008-08-05 16:19:09 as **
  • Effective Mast Cell Degranulating Peptide Inhibitors of the IgE/FcepsilonRI Receptor Interaction.
    Chemical biology & drug design (3 July 2008)
    by Angeliki Buku, Inna Keselman, Dmitry Lupyan, Mihaly Mezei, Joseph A A Price
    posted to ige ige-receptor mcd md peptide simulation by dimka on 2008-07-29 21:44:13 as ** along with 1 person yanz
  • Combined Electrostatics and Hydrogen Bonding Determine Intermolecular Interactions Between Polyphosphoinositides
    J. Am. Chem. Soc., Vol. 130, No. 28. (16 July 2008), pp. 9025-9030.
    by Ilya Levental, Andrejs Cebers, Paul A Janmey
    posted to pip2 sequestering by dimka on 2008-07-25 17:17:27 as **
  • Potassium channels: Possible new therapeutic targets in Parkinson's disease.
    Medical hypotheses (21 July 2008)
    by Yan Wang, Peng-Lin L Yang, Ji-Fei F Tang, Jia-Feng F Lin, Xiao-Hong H Cai, Xiao-Tong T Wang, Guo-Qing Q Zheng
    posted to desease kir review by dimka on 2008-07-25 17:14:02 as **
  • Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
    Supercomputing, 2006. SC '06. Proceedings of the ACM/IEEE SC 2006 Conference (2006), pp. 43-43.
    by KJ Bowers, E Chow, Huafeng Xu, RO Dror, MP Eastwood, BA Gregersen, JL Klepeis, I Kolossvary, MA Moraes, FD Sacerdoti, JK Salmon, Yibing Shan, DE Shaw
    posted to algorithm desmond engine md by dimka on 2008-07-24 19:09:14 as **
  • Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations
    Biophys. J. (9 May 2008), biophysj.107.121160.
    by Philip D Blood, Richard D Swenson, Gregory A Voth
    posted to md pip2 by dimka on 2008-07-24 18:37:03 as **
  • The Membrane Potential and its Representation by a Constant Electric Field in Computer Simulations.
    Biophysical journal (18 July 2008)
    by Benoit Roux
    posted to emf implicit membrane potential by dimka on 2008-07-22 18:57:28 as ** along with 1 person and 1 group abebe McCammon
  • Gabapentin activates ROMK1 channels by a protein kinase A (PKA)-dependent mechanism
    Br J Pharmacol, Vol. 154, No. 1. (3 March 2008), pp. 216-225.
    by CH Lee, TS Tsai, HH Liou
    posted to kir11 pip2 romk by dimka on 2008-07-21 17:42:53 as **
  • Mechanism of Na+/H+ Antiporting
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 799-803.
    by Isaiah T Arkin, Huafeng Xu, Morten O Jensen, Eyal Arbely, Estelle R Bennett, Kevin J Bowers, Edmond Chow, Ron O Dror, Michael P Eastwood, Ravenna Flitman-Tene, Brent A Gregersen, John L Klepeis, Istvan Kolossvary, Yibing Shan, David E Shaw
    posted to desmond md membrane simulation by dimka on 2008-07-08 21:34:50 as ** along with 4 people and 1 group sobolevnrm Jporci MMehrotra LamBras baker-group
  • 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 kirbac lipids md selectivity simulation 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 dppc gromacs md simulations 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 compare md membrane protein simulation 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 elastic enm motion protein by dimka on 2008-06-10 19:49:58 as ** along with 2 people simone 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 inositiol md phosphoinositides protein-ligand protein-lipid protein-membrane simulations 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 phosphoinositides pip2 pip3 synthesis 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 deltag free-energy lipids membrane 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 electrostatics marcks pip2 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 pip2 sequestering 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 blocker gating kcsa kir kv13 ph 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 hinge md-analysis 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 density md-analysis rdf simulaid 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 dynamics md md-analysis pca simulations by dimka on 2008-05-14 01:42:48 as ** along with 8 people and 1 group baaden aqeel yongzhao ttjoseph ffranca allmensch carlescorbi nigham TSRI_MGL
  • Simulaid
    http://atlas.physbio.mssm.edu/~mezei/simulaid/
    by Mihaly Mezei
    posted to analysis md md-analysis simulaid 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 katp kir md simulations 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 area lipid lipid-area nmr 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 dppc experimental lipid-order-parameter scd 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 lipid md nanotube perturbation simulation by dimka on 2008-05-13 21:14:16 as ** along with 2 people Marine 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 coarse-grain force-field md simulations by dimka on 2008-05-13 21:10:45 as ** along with 4 people and 1 group Marine choonpeng softsimu sunnytov Molecular dynamics in MSU
  • 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 charged implicit-water md simulations 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 implicit implicit-membrane membrane model by dimka on 2008-05-13 20:56:12 as ** along with 1 person onufriev
  • 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 kcsa mthk open-closed ph-sensor 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 compare electrostatic interaction protein-ligand 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 drug-design electrostatic electrostatic-complementarity ligand 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 distribution organization rdf sdf by dimka on 2008-05-12 19:15:25 as **
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