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Tag solvation [319 articles]

Recent papers classified by the tag solvation.
  • notes Solvation parameters for amino acids
    Journal of Computational Chemistry, Vol. 20, No. 4. (1999), pp. 428-442.
    by Brian J Smith
    posted to solvation modeling by xdeupi on 2007-01-12 12:48:19 as ** along with 1 person and 1 group papatonyhill LabCompMed
  • Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: On the correlation between crystal water sites, solvent density, and solvent dipole
    Journal of Computational Chemistry, Vol. 23, No. 14. (2002), pp. 1323-1336.
    by Junichi Higo, Masayoshi Nakasako
    posted to d20 hydration solvation water by softsimu on 2008-04-03 22:16:49 as **
  • Minimizing frustration by folding in an aqueous environment
    Archives of Biochemistry and Biophysics, Vol. 469, No. 1. (1 January 2008), pp. 118-131.
    by Carla Mattos, Clay A Clark
    posted to folding solvation water by softsimu on 2008-04-03 22:12:20 as **
  • Large-scale networks of hydration water molecules around bovine [beta]-trypsin revealed by cryogenic X-ray crystal structure analysis
    Journal of Molecular Biology, Vol. 289, No. 3. (11 June 1999), pp. 547-564.
    by Masayoshi Nakasako
    posted to d20 solvation water by softsimu on 2008-04-03 22:10:22 as **
  • Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation
    Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 4. (2007), pp. 804-813.
    by Takashi Imai, Ryusuke Hiraoka, Andriy Kovalenko, Fumio Hirata
    posted to solvation water by softsimu on 2008-04-03 22:09:23 as **
  • Microphase separation in a mixture of ionic and nonionic liquids
    J Phys Chem B, Vol. 111, No. 34. (2007), pp. 10189-10193.
    by AA Aerov, AR Khokhlov, II Potemkin
    posted to ions solvation by softsimu on 2008-01-14 13:34:38 as ** along with 1 person mrizal
  • Solubility of small molecule in ionic liquids: A model study on the ionic size effect
    J Phys Chem B, Vol. 111, No. 45. (2007), pp. 13047-13051.
    by P Lou, S Kang, KC Ko, JY Lee
    posted to ions solvation by softsimu on 2008-01-14 13:33:23 as ** along with 1 person mrizal
  • Molecular dynamics -- potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels
    Biophysical Chemistry, Vol. 124, No. 3. (1 December 2006), pp. 251-267.
    by Toby W Allen, Olaf S Andersen, Benoit Roux
    posted to biomembranes electrostatics molecular_dynamics molecular_simulation solvation by sobolevnrm on 2007-09-18 22:11:10 as read along with 2 people and 3 groups ibuch barry structural_bioinformatics Bioinformatics baker-group
  • Treatment of charge singularities in implicit solvent models
    The Journal of Chemical Physics, Vol. 127, No. 11. (2007)
    by Weihua Geng, Sining Yu, Guowei Wei
    posted to electrostatics mathematics solvation by sobolevnrm on 2007-09-25 12:45:23 as read along with 1 group baker-group
  • Interplay of ion binding and attraction in DNA condensed by multivalent cations
    Nucl. Acids Res., Vol. 36, No. 2. (2 February 2008), pp. 501-510.
    by Brian A Todd, Donald C Rau
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-02-29 12:40:03 as read along with 1 person and 2 groups skoch3 Koch_Lab baker-group
  • Aqueous Electrolytes near Hydrophobic Surfaces: Dynamic Effects of Ion Specificity and Hydrodynamic Slip
    Langmuir (6 December 2007)
    by DM Huang, C Cottin-Bizonne, C Ybert, L Bocquet
    posted to diffusion electrostatics solvation by sobolevnrm on 2008-01-11 12:58:36 as read along with 1 group baker-group
  • Continuum Solvent Modeling of Nonpolar Solvation: Improvement by Separating Surface Area Dependent Cavity and Dispersion Contributions
    J. Phys. Chem. A, Vol. 107, No. 16. (24 April 2003), pp. 3000-3004.
    by M Zacharias
    posted to nonpolar solvation by sobolevnrm on 2008-01-11 12:52:09 as read along with 1 person and 1 group dmobley baker-group
  • Observation of Immobilized Water Molecules around Hydrophobic Groups
    Physical Review Letters, Vol. 99, No. 14. (2007)
    by YLA Rezus, HJ Bakker
    posted to experimental_methodology nonpolar solvation by sobolevnrm on 2007-10-24 13:31:37 as read along with 3 people and 1 group dchen Cristiano Diego_Prada baker-group
  • Theory for an order-driven disruption of the liquid state in water
    The Journal of Chemical Physics, Vol. 128, No. 4. (2008)
    by Jeremy L England, Sanghyun Park, Vijay S Pande
    posted to molecular_dynamics solvation by sobolevnrm on 2008-02-29 12:20:30 as read along with 1 person and 1 group dmobley baker-group
  • Specific Ion Effects on Interfacial Water Structure near Macromolecules
    J. Am. Chem. Soc., Vol. 129, No. 40. (10 October 2007), pp. 12272-12279.
    by X Chen, T Yang, S Kataoka, PS Cremer
    posted to electrostatics solvation by sobolevnrm on 2007-10-08 12:42:30 as read along with 1 group baker-group
  • New and Original pKa Prediction Method Using Grid Molecular Interaction Fields
    J. Chem. Inf. Model. (2 October 2007)
    by F Milletti, L Storchi, G Sforna, G Cruciani
    posted to drug_design pka solvation by sobolevnrm on 2007-10-08 12:24:55 as read along with 1 person and 1 group sim82 baker-group
  • Effect of Solutes on the Structure and Energetics of a Model Solvent
    J. Phys. Chem. C, Vol. 111, No. 43. (1 November 2007), pp. 16060-16069.
    by P Degregorio, B Widom
    posted to solvation statistical_mechanics by sobolevnrm on 2007-10-30 11:25:18 as read along with 1 group baker-group
  • Specific Ion Adsorption and Surface Forces in Colloid Science
    J. Phys. Chem. B, Vol. 112, No. 6. (14 February 2008), pp. 1580-1585.
    by ERA Lima, D Horinek, RR Netz, EC Biscaia, FW Tavares, W Kunz, M Bostrom
    posted to biomembranes electrostatics interfaces solvation by sobolevnrm on 2008-02-20 12:39:17 as ** along with 1 group baker-group
  • Investigating interactions between HIV-1 gp41 and inhibitors by molecular dynamics simulation and MM-PBSA/GBSA calculations
    Journal of Molecular Structure: THEOCHEM, Vol. 766, No. 2-3. (15 August 2006), pp. 77-82.
    by Jian J Tan, Wei Z Chen, Cun X Wang
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 14:11:48 as read along with 1 group baker-group
  • Electrostatic Contributions to the Stability of the GCN4 Leucine Zipper Structure
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by William M Matousek, Barbara Ciani, Carolyn A Fitch, Bertrand E Garcia-Moreno, Richard A Kammerer, Andrei T Alexandrescu
    posted to electrostatics pka solvation by sobolevnrm on 2007-09-17 01:56:00 as read along with 1 person and 1 group cjeans baker-group
  • Charge Asymmetries in Hydration of Polar Solutes
    J. Phys. Chem. B (6 February 2008)
    by DL Mobley, AE Barber, CJ Fennell, KA Dill
    posted to electrostatics molecular_simulation solvation by sobolevnrm on 2008-03-03 12:35:35 as read along with 3 people and 1 group onufriev dmobley middledomain baker-group
  • Dielectric Properties Tangential to the Interface in Model Insoluble Monolayers: Theoretical Assessment
    Langmuir, Vol. 24, No. 9. (6 May 2008), pp. 4615-4624.
    by PG Shushkov, SA Tzvetanov, AN Ivanova, AV Tadjer
    posted to solvation electrostatics biomembranes by sobolevnrm on 2008-05-07 11:28:13 as read along with 1 group baker-group
  • PEG as a tool to gain insight into membrane fusion.
    Eur Biophys J, Vol. 36, No. 4-5. (April 2007), pp. 315-326.
    by BR Lentz
    posted to solvation biomembranes by sobolevnrm on 2008-05-07 11:25:44 as read along with 1 person and 1 group paulschlesinger baker-group
  • Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory
    The Journal of Chemical Physics, Vol. 128, No. 18. (2008)
    by Yoshiteru Yonetani, Yutaka Maruyama, Fumio Hirata, Hidetoshi Kono
    posted to solvation nucleic_acids integral_equation electrostatics by sobolevnrm on 2008-06-27 12:08:04 as read along with 1 group baker-group
  • Debye-Hückel theory of mixed charged-zwitterionic lipid layers
    The European Physical Journal E - Soft Matter, Vol. 26, No. 3. (17 July 2008), pp. 251-260.
    by D Mengistu, S May
    posted to solvation electrostatics biomembranes by sobolevnrm on 2008-06-27 12:06:38 as read along with 1 group baker-group
  • Theory of Dielectric Relaxation in Polar Liquids
    The Journal of Chemical Physics, Vol. 52, No. 12. (1970), pp. 6353-6363.
    by Tsu W Nee, Robert Zwanzig
    posted to statistical_mechanics solvation electrostatics diffusion by sobolevnrm on 2008-07-17 22:39:18 as read along with 1 group baker-group
  • Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?
    Journal of Computational Chemistry, Vol. 27, No. 16. (2006), pp. 1990-2007.
    by Christopher S Page, Paul A Bates
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 13:54:18 as read along with 1 group baker-group
  • Energetics of hydrophobic matching in lipid-protein interactions
    Biophys. J. (30 January 2008), biophysj.107.121475.
    by Derek Marsh
    posted to biomembranes protein-membrane_interactions solvation by sobolevnrm on 2008-03-03 12:23:57 as read along with 1 person and 1 group paulschlesinger baker-group
  • The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
    Biopolymers, Vol. 68, No. 1. (January 2003), pp. 47-62.
    by JH Lin, AL Perryman, JR Schames, JA McCammon
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 13:47:44 as read along with 4 people and 3 groups barry blackbart kazemi LamBras structural_bioinformatics Bioinformatics baker-group
  • Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects
    Biophys. J. (25 January 2008), biophysj.107.116335.
    by Sun-Joo Lee, Yuhua Song, Nathan A Baker
    posted to biomembranes electrostatics solvation by sobolevnrm on 2008-03-03 12:21:23 as read along with 1 person and 1 group paulschlesinger baker-group
  • Molecular mechanics PBSA ligand binding energy and interaction of Efavirenz derivatives with HIV-1 reverse transcriptase
    Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 20, No. 2. (2005), pp. 129-134.
    by Philip Weinzinger, Sup Hannongbua, Pete Wolschann
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 13:43:25 as **
  • Formation of a Wrapped DNA-Protein Interface: Experimental Characterization and Analysis of the Large Contributions of Ions and Water to the Thermodynamics of Binding IHF to H' DNA
    Journal of Molecular Biology, Vol. 377, No. 1. (14 March 2008), pp. 9-27.
    by Vander, Ruth M Saecker, Record
    posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm on 2008-03-03 12:04:18 as read along with 1 group baker-group
  • Dynamics of single-file water chains inside nanoscale channels: physics, biological significance and applications
    Journal of Physics D: Applied Physics, Vol. 41, No. 10. (2008), 103002.
    by Haiping Fang, Rongzheng Wan, Xiaojing Gong, Hangjun Lu, Songyan Li
    posted to thrombin solvation nanotech by sobolevnrm on 2008-04-23 11:01:51 as read along with 1 group baker-group
  • Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy
    J. Am. Chem. Soc., Vol. 130, No. 8. (27 February 2008), pp. 2374-2375.
    by S Ebbinghaus, SJ Kim, M Heyden, X Yu, M Gruebele, DM Leitner, M Havenith
    posted to kinetics protein_folding solvation by sobolevnrm on 2008-03-03 11:46:31 as read along with 1 group baker-group
  • An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Christina L Vizcarra, Naigong Zhang, Shannon A Marshall, Ned S Wingreen, Chen Zeng, Stephen L Mayo
    posted to electrostatics protein_engineering solvation by sobolevnrm on 2008-01-21 12:56:17 as read along with 1 group 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 nucleic_acids solvation by sobolevnrm on 2008-01-21 12:55:09 as read along with 3 people and 1 group dimka RamuAnandakrishnan onufriev baker-group
  • Solution of the Percus-Yevick equation for hard disks
    The Journal of Chemical Physics, Vol. 128, No. 18. (2008)
    by Adda M Bedia, E Katzav, D Vella
    posted to statistical_mechanics solvation integral_equation by sobolevnrm on 2008-07-08 12:19:31 as read along with 1 group baker-group
  • Specific Ion Adsorption at Hydrophobic Solid Surfaces
    Physical Review Letters, Vol. 99, No. 22. (2007)
    by Dominik Horinek, Roland R Netz
    posted to electrostatics interfaces solvation by sobolevnrm on 2008-01-25 12:47:45 as read along with 1 person and 1 group mikaellund baker-group
  • Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the Stability of RNA Hairpins
    J. Am. Chem. Soc., Vol. 130, No. 23. (11 June 2008), pp. 7364-7372.
    by David L Pincus, Changbong Hyeon, D Thirumalai
    posted to solvation nucleic_acids by sobolevnrm on 2008-07-08 11:59:21 as read along with 1 group baker-group
  • On the Manifestation of Hydrophobicity at the Nanoscale
    J. Phys. Chem. B (29 April 2008)
    by Niharendu Choudhury
    posted to solvation nonpolar by sobolevnrm on 2008-07-08 11:58:36 as read along with 1 person and 1 group paulschlesinger baker-group
  • Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation
    Proceedings of the National Academy of Sciences, Vol. 104, No. 44. (30 October 2007), pp. 17261-17265.
    by Lars Meinhold, Jeremy C Smith, Akio Kitao, Ahmed H Zewail
    posted to experimental_methodology molecular_dynamics protein_folding solvation by sobolevnrm on 2007-10-31 12:33:06 as read along with 1 group baker-group
  • Benchmarking pKa Prediction Methods for Residues in Proteins
    J. Chem. Theory Comput., Vol. 4, No. 6. (10 June 2008), pp. 951-966.
    by Courtney L Stanton, Kendall N Houk
    posted to solvation pka electrostatics by sobolevnrm on 2008-06-27 11:54:41 as read along with 1 group baker-group
  • Continuum molecular electrostatics, salt effects and counterion binding. A review of the Poisson-Boltzmann theory and its modifications.
    Biopolymers, Vol. 9999, No. 9999. (2007), NA.
    by Paweł Grochowski, Joanna Trylska
    posted to electrostatics solvation statistical_mechanics by sobolevnrm on 2007-10-31 12:22:56 as read along with 2 people and 1 group mikaellund softsimu baker-group
  • Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements
    J. Phys. Chem. B (22 September 2007)
    by AA Chen, RV Pappu
    posted to electrostatics molecular_simulation solvation by sobolevnrm on 2007-10-01 12:28:29 as read along with 1 person and 1 group middledomain baker-group
  • Coarse-Graining the Accessible Surface and the Electrostatics of Proteins for Protein-Protein Interactions
    J. Chem. Theory Comput. (24 August 2007)
    by F Pizzitutti, M Marchi, D Borgis
    posted to electrostatics multiscale solvation by sobolevnrm on 2007-08-27 12:22:06 as read along with 1 group baker-group
  • Improved p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> prediction: Combining empirical and semimicroscopic methods
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Gernot Kieseritzky, EW Knapp
    posted to solvation pka electrostatics bioinformatics by sobolevnrm on 2008-06-27 18:08:01 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • Hydrophobicity of protein surfaces: Separating geometry from chemistry
    Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2274-2279.
    by Nicolas Giovambattista, Carlos F Lopez, Peter J Rossky, Pablo G Debenedetti
    posted to electrostatics nonpolar solvation by sobolevnrm on 2008-03-13 11:36:43 as read along with 1 group baker-group
  • Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin
    Proceedings of the National Academy of Sciences, Vol. 93, No. 25. (10 December 1996), pp. 14526-14531.
    by William e Royer, Animesh Pardanani, Quentin h Gibson, Eric s Peterson, Joel m Friedman
    posted to allostery solvation by sobolevnrm on 2008-02-15 12:43:24 as read along with 1 group baker-group
  • Conformational Sampling of Peptides in Cellular Environments
    Biophys. J., Vol. 94, No. 3. (1 February 2008), pp. 747-759.
    by Seiichiro Tanizaki, Jacob Clifford, Brian D Connelly, Michael Feig
    posted to protein-membrane_interactions solvation by sobolevnrm on 2008-02-15 12:37:04 as read along with 1 group baker-group
  • K+/Na+ Selectivity in K Channels and Valinomycin: Over-coordination Versus Cavity-size constraints
    Journal of Molecular Biology, Vol. 376, No. 1. (8 February 2008), pp. 13-22.
    by Sameer Varma, Dubravko Sabo, Susan B Rempe
    posted to biomembranes ion_channels solvation thrombin by sobolevnrm on 2008-03-10 11:41:18 as read along with 1 group baker-group
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