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タグ: implicit_solvent [48 articles]

Recent papers classified by the tag implicit_solvent.
  • Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
    Journal of Biomolecular NMR, Vol. 22, No. 4. (1 April 2002), pp. 317-331.
    by Bin Xia, Vickie Tsui, David A Case, Jane H Dyson, Peter E Wright
    posted to implicit_solvent md by yxue on 2008-07-12 21:40:24 as **
  • Dielectric effects in biopolymers: The theory of ionic saturation revisited
    Biopolymers, Vol. 24, No. 3. (1985), pp. 427-439.
    by BE Hingerty, RH Ritchie, TL Ferrell, JE Turner
    posted to implicit_solvent by RamuAnandakrishnan on 2008-08-20 15:23:36 as **
  • Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model
    Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (2008), pp. 11146-11151.
    by Haipeng Gong, Glen Hocky, Karl F Freed
    posted to gb implicit_solvent pka by RamuAnandakrishnan on 2008-08-23 04:45:35 as **
  • Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
    J. Phys. Chem. A, Vol. 101, No. 43. (23 October 1997), pp. 8098-8106.
    by M Scarsi, J Apostolakis, A Caflisch
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:27:35 as ** along with 1 person onufriev
  • Improving implicit solvent simulations: a Poisson-centric view.
    Curr Opin Struct Biol, Vol. 15, No. 2. (April 2005), pp. 137-143.
    by NA Baker
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-03 20:08:08 as ** along with 2 people ttjoseph qwermish
  • The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
    Journal of Computational Chemistry, Vol. 29, No. 12. (2008), pp. 1970-1981.
    by Magdalena Gruziel, Pawel Grochowski, Joanna Trylska
    posted to implicit_solvent by RamuAnandakrishnan on 2008-08-03 15:54:27 as ** along with 1 person and 2 groups barry structural_bioinformatics McCammon
  • The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Paul Labute
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-02-28 17:07:10 as ** along with 6 people and 1 group onufriev sobolevnrm middledomain sunhwan dmobley GermanErlenkamp baker-group
  • An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications
    The Journal of Chemical Physics, Vol. 129, No. 7. (2008)
    by John C Gordon, Andrew T Fenley, Alexey Onufriev
    posted to implicit_solvent by RamuAnandakrishnan on 2008-08-22 23:53:40 as ** along with 1 person agrossfield
  • Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease
    Journal of Computational Chemistry, Vol. 21, No. 4. (2000), pp. 295-309.
    by Laurent David, Ray Luo, Michael K Gilson
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-09 20:25:06 as **
  • HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations.
    Proc Natl Acad Sci U S A, Vol. 103, No. 4. (24 January 2006), pp. 915-920.
    by V Hornak, A Okur, RC Rizzo, C Simmerling
    posted to amber implicit_solvent md by RamuAnandakrishnan on 2007-12-14 16:16:11 as ** along with 3 people aqeel allmensch choonpeng
  • Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions
    Biophys. J., Vol. 83, No. 1. (1 July 2002), pp. 382-406.
    by Lihua Wang, Brian E Hingerty, AR Srinivasan, Wilma K Olson, Suse Broyde
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-17 16:03:35 as **
  • 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 electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-13 13:11:53 as ** along with 3 people and 1 group sobolevnrm onufriev dimka baker-group
  • Recent advances in the development and application of implicit solvent models in biomolecule simulations.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 217-224.
    by M Feig, CL Brooks
    posted to implicit_solvent md by RamuAnandakrishnan on 2007-11-28 21:18:14 as ** along with 5 people and 2 groups apostola simone ttjoseph marcius gane5h BioinfoCIPF SGU-CIPF
  • The Amber biomolecular simulation programs.
    J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1668-1688.
    by DA Case, TE Cheatham, T Darden, H Gohlke, R Luo, KM Merz, A Onufriev, C Simmerling, B Wang, RJ Woods
    posted to amber explicit_solvent implicit_solvent md by RamuAnandakrishnan on 2007-12-14 15:57:53 as ** along with 10 people and 3 groups lna jwm ttjoseph xdeupi tovrstra bilab IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
  • Generalized Born Model with a Simple, Robust Molecular Volume Correction
    J. Chem. Theory Comput., Vol. 3, No. 1. (9 January 2007), pp. 156-169.
    by J Mongan, C Simmerling, JA Mccammon, DA Case, A Onufriev
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 22:43:38 as **
  • Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design
    BMC Bioinformatics, Vol. 9 (13 March 2008), 148.
    by Marcel, Anne Lopes, Najette Amara, Christine Bathelt, Thomas Simonson
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-13 22:36:35 as ** along with 1 person GeeSharpMinor
  • Free energy landscape of protein folding in water: Explicit vs. implicit solvent
    Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (2003), pp. 148-161.
    by Ruhong Zhou
    posted to electrostatics folding implicit_solvent md by RamuAnandakrishnan on 2007-11-03 15:33:23 as ** along with 3 people choonpeng onufriev msuarezdiez
  • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    Journal of Computational Chemistry, Vol. 9, No. 4. (1988), pp. 327-335.
    by Michael K Gilson, Kim A Sharp, Barry H Honig
    posted to electrostatics implicit_solvent by RamuAnandakrishnan on 2008-04-21 15:11:03 as **
  • Theory and applications of the generalized born solvation model in macromolecular simulations
    Biopolymers, Vol. 56, No. 4. (4 December 2001), pp. 275-291.
    by Vickie Tsui, David A Case
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-03 21:38:04 as ** along with 1 person ttjoseph
  • Proton Binding to Proteins: p<i>K</i><sub>a</sub> Calculations with Explicit and Implicit Solvent Models
    J. Am. Chem. Soc., Vol. 126, No. 13. (7 April 2004), pp. 4167-4180.
    by T Simonson, J Carlsson, DA Case
    posted to electrostatics explicit_solvent implicit_solvent pka by RamuAnandakrishnan on 2008-03-28 18:39:53 as ** along with 3 people and 1 group 6rheology sobolevnrm dmobley baker-group
  • Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.
    Protein science : a publication of the Protein Society, Vol. 1, No. 9. (September 1992), pp. 1185-1205.
    by J Guenot, PA Kollman
    posted to explicit_solvent implicit_solvent md by RamuAnandakrishnan on 2008-08-20 15:06:48 as **
  • Theory of electrostatic interactions in macromolecules
    Current Opinion in Structural Biology, Vol. 5, No. 2. (April 1995), pp. 216-223.
    by Michael K Gilson
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:23:25 as **
  • Generalized born models of macromolecular solvation effects.
    Annu Rev Phys Chem, Vol. 51 (2000), pp. 129-152.
    by D Bashford, DA Case
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-03 20:02:52 as ** along with 1 person dgront
  • Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Michael D Altman, Jaydeep P Bardhan, Jacob K White, Bruce Tidor
    posted to electrostatics implicit_solvent by RamuAnandakrishnan on 2008-07-15 02:40:59 as **
  • Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study
    Biophysical Chemistry, Vol. 78, No. 1-2. (5 April 1999), pp. 69-88.
    by PH Hunenberger, JA Mccammon
    posted to electrostatics ewald implicit_solvent md by RamuAnandakrishnan on 2007-12-03 21:02:33 as **
  • Bending of DNA by Asymmetric Charge Neutralization: All-Atom Energy Simulations
    J. Am. Chem. Soc., Vol. 124, No. 17. (1 May 2002), pp. 4838-4847.
    by KM Kosikov, AA Gorin, XJ Lu, WK Olson, GS Manning
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-17 16:06:20 as **
  • Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
    The Journal of Chemical Physics, Vol. 124, No. 12. (2006)
    by Grigori Sigalov, Andrew Fenley, Alexey Onufriev
    posted to electrostatics implicit_solvent by RamuAnandakrishnan on 2007-12-05 20:45:46 as ** along with 1 person Elena_Zubova
  • Accelerated Poisson-Boltzmann calculations for static and dynamic systems
    Journal of Computational Chemistry, Vol. 23, No. 13. (17 July 2002), pp. 1244-1253.
    by Ray Luo, Laurent David, Michael K Gilson
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:43:42 as **
  • An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis
    The Journal of Chemical Physics, Vol. 129, No. 7. (2008)
    by Andrew T Fenley, John C Gordon, Alexey Onufriev
    posted to pb implicit_solvent by RamuAnandakrishnan on 2008-09-09 16:52:12 as ** along with 2 people afenley agrossfield
  • AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
    Journal of Computational Chemistry, Vol. 25, No. 4. (2004), pp. 479-499.
    by Emilio Gallicchio, Ronald M Levy
    posted to implicit_solvent gb by RamuAnandakrishnan on 2008-09-09 19:44:55 as ** along with 2 people jwagoner onufriev
  • Simulation of the Folding Equilibrium of α-Helical Peptides: A Comparison of the Generalized Born Approximation with Explicit Solvent
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 24. (2003), pp. 13934-13939.
    by Hugh Nymeyer, Angel E García
    posted to pb implicit_solvent gb by RamuAnandakrishnan on 2008-09-09 20:14:57 as **
  • Classical Electrostatics in Biology and Chemistry
    Science, Vol. 268 (1995), pp. 1144-1147.
    by Barry Honig, Anthony Nicholls
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:17:00 as ** along with 1 person qwermish
  • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.
    J Mol Biol, Vol. 235, No. 3. (21 January 1994), pp. 983-1002.
    by R Abagyan, M Totrov
    posted to electrostatics folding implicit_solvent statistical_mechanics by RamuAnandakrishnan on 2008-02-28 17:47:39 as ** along with 2 people bluvsh1 sigalov
  • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    Journal of Computational Chemistry, Vol. 12, No. 4. (1991), pp. 435-445.
    by Anthony Nicholls, Barry Honig
    posted to pb implicit_solvent by RamuAnandakrishnan on 2008-10-03 22:56:36 as **
  • Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 13934-13939.
    by H Nymeyer, AE García
    posted to electrostatics explicit_solvent folding implicit_solvent md by RamuAnandakrishnan on 2007-11-05 15:38:32 as ** along with 1 person fjc1
  • Computational prediction of the binding site of proteinase 3 to the plasma membrane
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Eric Hajjar, Maja Mihajlovic, Véronique Witko-Sarsat, Themis Lazaridis, Nathalie Reuter
    posted to binding_site electrostatics implicit_solvent ligand md by RamuAnandakrishnan on 2008-01-07 14:43:43 as **
  • Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
    Journal of Molecular Biology, Vol. 224, No. 2. (20 March 1992), pp. 473-486.
    by Donald Bashford, Klaus Gerwert
    posted to electrostatics implicit_solvent pka by RamuAnandakrishnan on 2008-06-22 18:37:19 as **
  • Electrostatic Interactions in Macromolecules: Theory and Applications
    Annual Review of Biophysics and Biophysical Chemistry, Vol. 19, No. 1. (1990), pp. 301-332.
    by KA Sharp, B Honig
    posted to pb implicit_solvent by RamuAnandakrishnan on 2008-10-03 22:51:17 as **
  • Macromolecular electrostatics: continuum models and their growing pains
    Current Opinion in Structural Biology, Vol. 11, No. 2. (1 April 2001), pp. 243-252.
    by Thomas Simonson
    posted to implicit_solvent md by RamuAnandakrishnan on 2007-11-28 20:47:25 as **
  • Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Anna CV Johansson, Erik Lindahl
    posted to electrostatics explicit_solvent implicit_solvent md by RamuAnandakrishnan on 2007-12-16 15:17:13 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Continuum Electrostatics Fails to Describe Ion Permeation in the Gramicidin Channel
    Biophys. J., Vol. 83, No. 3. (1 September 2002), pp. 1348-1360.
    by Scott Edwards, Ben Corry, Serdar Kuyucak, Shin-Ho Chung
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-28 18:31:12 as **
  • Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules--applications in biotechnology.
    Biotechnol Annu Rev, Vol. 9 (2003), pp. 315-395.
    by MT Neves-Petersen, SB Petersen
    posted to electrostatics implicit_solvent pka statistical_mechanics by RamuAnandakrishnan on 2007-11-15 21:40:25 as **
  • Electrostatics calculations: latest methodological advances.
    Curr Opin Struct Biol, Vol. 16, No. 2. (13 March 2006), pp. 142-151.
    by Patrice Koehl
    posted to electrostatics explicit_solvent implicit_solvent md by RamuAnandakrishnan on 2007-11-03 15:41:21 as ** along with 3 people BragilMassoud qwermish jteyra
  • Multiscale modeling and simulation methods with applications to dendritic polymers
    Computational and Theoretical Polymer Science, Vol. 11, No. 5. (October 2001), pp. 345-356.
    by Tahir Cagin, Guofeng Wang, Ryan Martin, Georgios Zamanakos, Nagarajan Vaidehi, Daniel T Mainz, William A Goddard
    posted to coarse_grain implicit_solvent md by RamuAnandakrishnan on 2007-12-02 15:00:44 as **
  • Accelerating molecular dynamic simulation on the cell processor and playstation 3
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Edgar Luttmann, Daniel L Ensign, Vishal Vaidyanathan, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark Friedrichs, Vijay S Pande
    posted to implicit_solvent md by RamuAnandakrishnan on 2008-07-15 02:39:04 as **
  • Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Magne Olufsen, Elena Papaleo, Arne O Smalås, Bjørn O Brandsdal
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-11-15 19:44:01 as ** along with 2 people camster gisle
  • Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.
    Proteins, Vol. 60, No. 3. (15 August 2005), pp. 464-484.
    by X Li, SA Hassan, EL Mehler
    posted to cgreview implicit_solvent by baaden on 2005-07-31 12:08:58 as **
  • Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
    The Journal of Chemical Physics, Vol. 119, No. 9. (2003), pp. 4817-4826.
    by Tomasz Grycuk
    posted to force_fields gb implicit_solvent by baaden on 2007-08-10 15:22:29 as ** along with 1 person onufriev
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