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RamuAnandakrishnan's electrostatics [65 articles]

当前文献位于 RamuAnandakrishnan's 文献库 标签分类为 electrostatics. You can also see everyone's electrostatics.
  • 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 **
  • Calculating pKa values in enzyme active sites
    Protein Sci, Vol. 12, No. 9. (1 September 2003), pp. 1894-1901.
    by Jens E Nielsen, Andrew J Mccammon
    posted to electrostatics pka statistical_mechanics by RamuAnandakrishnan on 2008-06-30 00:49:34 as ** along with 3 people and 1 group tny boris_aguilar qaiser_fatmi group
  • 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 **
  • Atomic charges derived from electrostatic potentials: A detailed study
    Journal of Computational Chemistry, Vol. 8, No. 6. (1987), pp. 894-905.
    by Lisa E Chirlian, Michelle M Francl
    posted to electrostatics md by RamuAnandakrishnan on 2008-06-20 23:08:59 as **
  • Protein model refinement using an optimized physics-based all-atom force field
    Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273.
    by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick
    posted to amber electrostatics folding by RamuAnandakrishnan on 2008-06-19 12:23:29 as ** along with 3 people and 2 groups jmccammon barry zwang structural_bioinformatics McCammon
  • Some fundamental problems for an energy-conserving adaptive-resolution molecular dynamics scheme
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 4. (2007)
    by Luigi Delle Site
    posted to cutoff electrostatics md by RamuAnandakrishnan on 2008-06-02 23:22:52 as **
  • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.
    Science, Vol. 282, No. 5389. (23 October 1998), pp. 740-744.
    by Y Duan, PA Kollman
    posted to electrostatics folding md by RamuAnandakrishnan on 2008-05-28 21:44:59 as ** along with 3 people j3xucite allmensch choonpeng
  • Very fast prediction and rationalization of pKa values for protein-ligand complexes
    Proteins, Vol. 9999 (2008)
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to electrostatics ligand pka by RamuAnandakrishnan on 2008-05-25 13:40:07 as **
  • Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
    Annual Review of Physical Chemistry, Vol. 59, No. 1. (2008), pp. 545-571.
    by Matej Praprotnik, Luigi Delle Site, Kurt Kremer
    posted to coarse_grain electrostatics md by RamuAnandakrishnan on 2008-05-21 13:42:03 as ** along with 1 person softsimu
  • Improved pKa prediction: Combining empirical and semimicroscopic methods
    Journal of Computational Chemistry, Vol. 9999 (2008)
    by Gernot Kieseritzky, EW Knapp
    posted to electrostatics pka by RamuAnandakrishnan on 2008-05-16 01:53:45 as **
  • pKD: re-designing protein pKa values
    Nucleic Acids Research, Vol. 34, No. web server issue., pp. W48-W51.
    by Barbara M Tynan-Connolly, Jens E Nielsen
    posted to electrostatics pka by RamuAnandakrishnan on 2008-04-28 02:07:11 as **
  • Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Timothy J Giese, Darrin M York
    posted to electrostatics explicit_solvent multipole by RamuAnandakrishnan on 2008-04-24 13:50:18 as ** along with 1 person middledomain
  • 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 **
  • Some fundamental problems for an energy conserving adaptive resolution molecular dynamics scheme
    (17 Sep 2007)
    by L Delle Site
    posted to coarse_grain electrostatics md by RamuAnandakrishnan on 2008-04-16 20:41:19 as **
  • 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
  • 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 **
  • Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
    Journal of Computational Chemistry, Vol. 23, No. 13. (2002), pp. 1211-1219.
    by Pekka Mark, Lennart Nilsson
    posted to cutoff electrostatics md by RamuAnandakrishnan on 2008-03-28 15:22:19 as **
  • Ewald summation techniques in perspective: a survey
    Computer Physics Communications, Vol. 95, No. 2-3. (June 1996), pp. 73-92.
    by Abdulnour Y Toukmaji, John A Board
    posted to electrostatics ewald by RamuAnandakrishnan on 2008-03-28 14:57:44 as ** along with 1 person softsimu
  • Convergence of molecular dynamics simulations of membrane proteins.
    Proteins (22 January 2007)
    by Alan Grossfield, Scott E E Feller, Michael C C Pitman
    posted to electrostatics md by RamuAnandakrishnan on 2008-03-24 14:34:24 as ** along with 2 people dimka nigham
  • 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 **
  • 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 **
  • 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
  • Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules
    Journal of Computational Biology, Vol. 15, No. 2. (2008), pp. 165-184.
    by Ramu Anandakrishnan, Alexey Onufriev
    posted to electrostatics pka statistical_mechanics by RamuAnandakrishnan on 2008-03-03 23:47:30 as ** along with 1 person eskay
  • 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
  • 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
  • Comments on PPPM, FMM, and the Ewald Method for Large Periodic Coulombic Systems
    (29 Nov 1995)
    by EL Pollock, Jim Glosli
    posted to electrostatics ewald multipole by RamuAnandakrishnan on 2008-02-23 17:21:25 as **
  • 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 **
  • pH sensitivity of type III secretion system tip proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron P Markham, Susan E Birket, William D Picking, Wendy L Picking, Russell C Middaugh
    posted to electrostatics folding pka by RamuAnandakrishnan on 2008-01-07 14:40:54 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
  • 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
  • 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
  • Convergence of molecular dynamics simulations of membrane proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 1. (2007), pp. 31-40.
    by Alan Grossfield, Scott E Feller, Michael C Pitman
    posted to electrostatics md by RamuAnandakrishnan on 2007-12-04 22:49:47 as **
  • Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
    Journal of Computational Chemistry, Vol. 23, No. 13. (2002), pp. 1211-1219.
    by Pekka Mark, Lennart Nilsson
    posted to cutoff electrostatics md by RamuAnandakrishnan on 2007-12-04 22:43:47 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
  • 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 **
  • Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
    Annu Rev Biophys Biomol Struct, Vol. 30 (2001), pp. 211-243.
    by W Wang, O Donini, CM Reyes, PA Kollman
    posted to electrostatics md by RamuAnandakrishnan on 2007-12-03 20:54:28 as ** along with 1 person ibuch
  • Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides
    Biochemistry, Vol. 44, No. 2. (18 January 2005), pp. 609-616.
    by DAC Beck, RS Armen, V Daggett
    posted to cutoff electrostatics md by RamuAnandakrishnan on 2007-12-03 20:40:03 as **
  • 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
  • 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
  • A generalized reaction field method for molecular dynamics simulations
    The Journal of Chemical Physics, Vol. 102, No. 13. (1995), pp. 5451-5459.
    by Ilario G Tironi, René Sperb, Paul E Smith, Wilfred F van Gunsteren
    posted to electrostatics md by RamuAnandakrishnan on 2007-12-02 18:01:20 as **
  • Blue matter: approaching the limits of concurrency for classical molecular dynamics
    (2006)
    by Blake G Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, Christopher TJ Ward, Mark Giampapa, Michael C Pitman, Robert S Germain
    posted to electrostatics md by RamuAnandakrishnan on 2007-11-30 17:13:55 as **
  • Molecular dynamics simulations of biomolecules: long-range electrostatic effects.
    Annu Rev Biophys Biomol Struct, Vol. 28 (1999), pp. 155-179.
    by C Sagui, TA Darden
    posted to electrostatics md by RamuAnandakrishnan on 2007-11-27 21:48:35 as ** along with 6 people onufriev lillekatt ttjoseph dgront AndreaColetta r2s2
  • Stability and dynamics of virus capsids described by coarse-grained modeling.
    Structure, Vol. 14, No. 12. (December 2006), pp. 1767-1777.
    by A Arkhipov, PL Freddolino, K Schulten
    posted to coarse_grain electrostatics folding md by RamuAnandakrishnan on 2007-11-22 04:42:33 as ** along with 1 person choonpeng
  • 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 **
  • BIOMOLECULAR SIMULATIONS: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions
    - Annual Review of Biophysics and Biomolecular Structure, Vol. 30, No. 1. (2001), 211.
    by Wei
    posted to electrostatics md by RamuAnandakrishnan on 2007-11-15 20:19:24 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
  • ESPResSo--an extensible simulation package for research on soft matter systems
    Computer Physics Communications, Vol. 174, No. 9. (1 May 2006), pp. 704-727.
    by HJ Limbach, A Arnold, BA Mann, C Holm
    posted to electrostatics md by RamuAnandakrishnan on 2007-11-14 16:12:04 as ** along with 2 people softsimu pawelp
  • Coarse grain models and the computer simulation of soft materials
    Journal of Physics: Condensed Matter, Vol. 16, No. 15. (2004), pp. R481-R512.
    by Steve O Nielsen, Carlos F Lopez, Goundla Srinivas, Michael L Klein
    posted to electrostatics md by RamuAnandakrishnan on 2007-11-13 23:20:39 as ** along with 2 people kaz229 softsimu
  • Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site
    Physical Review Letters, Vol. 95, No. 21. (2005)
    by Marilisa Neri, Claudio Anselmi, Michele Cascella, Amos Maritan, Paolo Carloni
    posted to electrostatics md by RamuAnandakrishnan on 2007-11-09 17:07:46 as **
  • Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins
    Journal of Computational Chemistry, Vol. 16, No. 11. (1995), pp. 1357-1377.
    by Piotr Cieplak, Wendy D Cornell, Christopher Bayly, Peter A Kollman
    posted to electrostatics force_field by RamuAnandakrishnan on 2007-11-05 17:06:11 as ** along with 2 people easybakemuffin AndreaColetta
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