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Group: baker-group - with tag solvation [1000+ articles]

Recent papers posted by members of the baker-group group with tag solvation
  • Liquid Crystalline Phase Behavior of High Molecular Weight DNA: A Comparative Study of the Influence of Metal Ions of Different Size, Charge and Binding Mode
    Biomacromolecules, Vol. 9, No. 7. (14 July 2008), pp. 1860-1869.
    by Neethu Sundaresan, Cherumuttathu H Suresh, Thresia Thomas, TJ Thomas, CKS Pillai
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-07-25 12:02:47 as read
  • Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study
    Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. 4634-4645.
    by Johan H Bredenberg, Cristina Russo, Marcia O Fenley
    posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2008-07-25 11:56:28 as read
  • A stringent test of the cavity concept in continuum dielectrics
    The Journal of Chemical Physics, Vol. 107, No. 19. (1997), pp. 7975-7978.
    by Arno Papazyan, Arieh Warshel
    posted to solvation electrostatics by sobolevnrm to the group baker-group on 2008-07-24 12:44:14 as read
  • Continuum and Dipole-Lattice Models of Solvation
    J. Phys. Chem. B, Vol. 101, No. 51. (18 December 1997), pp. 11254-11264.
    by A Papazyan, A Warshel
    posted to solvation electrostatics by sobolevnrm to the group baker-group on 2008-07-24 12:43:04 as read
  • Effect of Solvent Discreteness on Solvation
    J. Phys. Chem. B, Vol. 102, No. 27. (2 July 1998), pp. 5348-5357.
    by A Papazyan, A Warshel
    posted to statistical_mechanics solvation electrostatics by sobolevnrm to the group baker-group on 2008-07-24 12:41:40 as read
  • A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics
    J. Emerg. Technol. Comput. Syst., Vol. 4, No. 2. (April 2008), pp. 1-30.
    by Shih-Hsien Kuo, Bruce Tidor, Jacob White
    posted to solvation software mathematics electrostatics by sobolevnrm to the group baker-group on 2008-07-24 11:45:11 as read
  • 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. (2008)
    by Nobuyuki Matubayasi, Wataru Shinoda, Masaru Nakahara
    posted to statistical_mechanics solvation ligand-membrane_interactions biomembranes by sobolevnrm to the group baker-group on 2008-07-23 11:59:00 as read along with 2 people agrossfield paulschlesinger
  • Statistical mechanics of polar fluids in electric fields
    The Journal of Chemical Physics, Vol. 72, No. 3. (1980), pp. 1597-1613.
    by Ho JS Ye, G Stell
    posted to statistical_mechanics solvation electrostatics by sobolevnrm to the group baker-group on 2008-07-22 12:00:42 as read
  • Very fast prediction and rationalization of p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to solvation software pka electrostatics bioinformatics by sobolevnrm to the group baker-group on 2008-07-22 11:48:46 as read
  • Hydrodynamic modeling of diffusion tensor properties of flexible molecules
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Vincenzo Barone, Mirco Zerbetto, Antonino Polimeno
    posted to solvation diffusion by sobolevnrm to the group baker-group on 2008-07-22 11:43:12 as read
  • Test of the Gouy-Chapman Theory for a Charged Lipid Membrane against Explicit-Solvent Molecular Dynamics Simulations
    Physical Review Letters, Vol. 101, No. 3. (2008)
    by Myunggi Yi, Hugh Nymeyer, Huan X Zhou
    posted to solvation electrostatics biomembranes by sobolevnrm to the group baker-group on 2008-07-21 21:02:32 as read
  • Ion Specific Protein Assembly and Hydrophobic Surface Forces
    Physical Review Letters, Vol. 100, No. 25. (2008)
    by Mikael Lund, Pavel Jungwirth, Clifford E Woodward
    posted to solvation protein-protein_interactions nonpolar by sobolevnrm to the group baker-group on 2008-07-21 21:01:25 as read along with 1 person mikaellund
  • 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 to the group baker-group on 2008-07-17 22:39:18 as read
  • Electric Moments of Molecules in Liquids
    Journal of the American Chemical Society, Vol. 58, No. 8. (1936), pp. 1486-1493.
    by L Onsager
    posted to statistical_mechanics solvation electrostatics by sobolevnrm to the group baker-group on 2008-07-17 18:32:11 as read
  • Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane
    Biophys. J., Vol. 82, No. 1. (1 January 2002), pp. 76-92.
    by Christian Fleck, Roland R Netz, Hans H von Grunberg
    posted to solvation pka nucleic_acids electrostatics biomembranes by sobolevnrm to the group baker-group on 2008-07-16 16:02:21 as read along with 1 person softsimu
  • From the Cover: A dry ligand-binding cavity in a solvated protein
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6296-6301.
    by Johan Qvist, Monika Davidovic, Donald Hamelberg, Bertil Halle
    posted to solvation by sobolevnrm to the group baker-group on 2008-07-11 12:10:08 as read along with 2 people and 2 groups barry jmccammon McCammon structural_bioinformatics
  • Role of Backbone&#x2212;Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Proteins
    J. Am. Chem. Soc. (16 May 2008)
    by Hoang T Tran, Albert Mao, Rohit V Pappu
    posted to solvation protein_folding by sobolevnrm to the group baker-group on 2008-07-09 11:35:18 as read along with 1 person paulschlesinger
  • Dielectric relaxation in proteins: the computational perspective.
    Photosynthesis research (29 April 2008)
    by Thomas Simonson
    posted to solvation quantum_mechanics electrostatics by sobolevnrm to the group baker-group on 2008-07-09 11:33:04 as read along with 1 person dimka
  • Assessing the performance of implicit solvation models at a nucleic acid surface
    Physical Chemistry Chemical Physics (in press)
    by F Dong, JA Wagoner, NA Baker
    posted to solvation nucleic_acids nonpolar electrostatics by sobolevnrm to the group baker-group on 2008-07-08 12:27:15 as read
  • 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 to the group baker-group on 2008-07-08 12:19:31 as read
  • 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 to the group baker-group on 2008-07-08 11:59:21 as read
  • On the Manifestation of Hydrophobicity at the Nanoscale
    J. Phys. Chem. B (29 April 2008)
    by Niharendu Choudhury
    posted to solvation nonpolar by sobolevnrm to the group baker-group on 2008-07-08 11:58:36 as read along with 1 person paulschlesinger
  • Variable atomic radii for continuum-solvent electrostatics calculation
    The Journal of Chemical Physics, Vol. 129, No. 1. (2008)
    by Baojing Zhou, Manish Agarwal, Chung F Wong
    posted to solvation electrostatics by sobolevnrm to the group baker-group on 2008-07-07 11:52:16 as read
  • Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces
    Journal of Computational Physics, Vol. 224, No. 2. (10 June 2007), pp. 729-756.
    by Sining Yu, Yongcheng Zhou, GW Wei
    posted to solvation mathematics electrostatics by sobolevnrm to the group baker-group on 2008-07-01 02:31:14 as read
  • The minimal molecular surface
    (20 Oct 2006)
    by PW Bates, GW Wei, Shan Zhao
    posted to solvation mathematics electrostatics by sobolevnrm to the group baker-group on 2008-06-30 15:42:08 as read
  • Functionally Linked Hydration Changes in Escherichia coli Aspartate Transcarbamylase and Its Catalytic Subunit
    Biochemistry, Vol. 36, No. 33. (19 August 1997), pp. 10161-10167.
    by VJ Licata, NM Allewell
    posted to structure solvation by sobolevnrm to the group baker-group on 2008-06-30 15:39:25 as read
  • A Continuum Model for Protein-Protein Interactions: Application to the Docking Problem
    Journal of Molecular Biology, Vol. 250, No. 2. (7 July 1995), pp. 258-275.
    by Richard M Jackson, Michael J Sternberg
    posted to solvation protein-protein_interactions electrostatics by sobolevnrm to the group baker-group on 2008-06-30 15:37:33 as read along with 1 person cjeans
  • DNA Binding and Bending by HMG Boxes: Energetic Determinants of Specificity
    Journal of Molecular Biology, Vol. 343, No. 2. (15 October 2004), pp. 371-393.
    by Anatoly I Dragan, Christopher M Read, Elena N Makeyeva, Ekaterina I Milgotina, Mair E Churchill, Colyn Crane-Robinson, Peter L Privalov
    posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2008-06-30 15:33:24 as read
  • Absorption Classification of Oral Drugs Based on Molecular Surface Properties
    J. Med. Chem., Vol. 46, No. 4. (13 February 2003), pp. 558-570.
    by CAS Bergstrom, M Strafford, L Lazorova, A Avdeef, K Luthman, P Artursson
    posted to solvation electrostatics drug_design bioinformatics by sobolevnrm to the group baker-group on 2008-06-30 15:29:07 as read
  • The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures
    Journal of Molecular Biology, Vol. 228, No. 1. (5 November 1992), pp. 13-22.
    by Leslie A Kuhn, Michael A Siani, Michael E Pique, Cindy L Fisher, Elizabeth D Getzoff, John A Tainer
    posted to structure solvation bioinformatics by sobolevnrm to the group baker-group on 2008-06-30 15:25:55 as read
  • Analytical molecular surface calculation
    Journal of Applied Crystallography, Vol. 16, No. 5. (Oct 1983), pp. 548-558.
    by ML Connolly
    posted to solvation mathematics electrostatics by sobolevnrm to the group baker-group on 2008-06-30 12:50:46 as read along with 1 person sithmein
  • Areas, Volumes, Packing, and Protein Structure
    Annual Review of Biophysics and Bioengineering, Vol. 6, No. 1. (1977), pp. 151-176.
    by FM Richards
    posted to structure solvation electrostatics by sobolevnrm to the group baker-group on 2008-06-30 12:39:51 as read
  • Solvation Free Energy of Polar and Nonpolar Molecules in Water: An Extended Interaction Site Integral Equation Theory in Three Dimensions
    J. Phys. Chem. B, Vol. 104, No. 4. (3 February 2000), pp. 796-805.
    by Q Du, D Beglov, B Roux
    posted to statistical_mechanics solvation by sobolevnrm to the group baker-group on 2008-06-30 12:37:45 as read
  • Calculation of the aqueous solvation free energy of the proton
    The Journal of Chemical Physics, Vol. 109, No. 12. (1998), pp. 4852-4863.
    by GJ Tawa, IA Topol, SK Burt, RA Caldwell, AA Rashin
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2008-06-30 12:27:13 as read
  • Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules
    J. Chem. Theory Comput., Vol. 1, No. 1. (11 January 2005), pp. 70-77.
    by Y Takano, KN Houk
    posted to solvation quantum_mechanics by sobolevnrm to the group baker-group on 2008-06-30 12:23:59 as read
  • Solvation Free Energies of the Nucleic Acid Bases
    J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8587-8594.
    by JL Miller, PA Kollman
    posted to solvation nucleic_acids molecular_simulation by sobolevnrm to the group baker-group on 2008-06-30 12:15:23 as read
  • Linear-scaling semiempirical quantum calculations for macromolecules
    The Journal of Chemical Physics, Vol. 105, No. 7. (1996), pp. 2744-2750.
    by Tai S Lee, Darrin M York, Weitao Yang
    posted to solvation quantum_mechanics by sobolevnrm to the group baker-group on 2008-06-30 12:13:04 as read
  • Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field
    J. Phys. Chem. B, Vol. 102, No. 47. (19 November 1998), pp. 9571-9576.
    by B Jayaram, D Sprous, DL Beveridge
    posted to solvation molecular_simulation generalized_born by sobolevnrm to the group baker-group on 2008-06-30 12:10:27 as read
  • Scaling of Hydrophobic Solvation Free Energies
    J. Phys. Chem. B, Vol. 105, No. 28. (19 July 2001), pp. 6704-6709.
    by DM Huang, PL Geissler, D Chandler
    posted to statistical_mechanics solvation nonpolar by sobolevnrm to the group baker-group on 2008-06-30 12:07:43 as read
  • A QM/MM study combined with the theory of energy representation: Solvation free energies for anti/syn acetic acids in aqueous solution
    Chemical Physics Letters, Vol. 419, No. 1-3. (15 February 2006), pp. 240-244.
    by Takumi Hori, Hideaki Takahashi, Masayoshi Nakano, Tomoshige Nitta, Weitao Yang
    posted to solvation quantum_mechanics by sobolevnrm to the group baker-group on 2008-06-30 12:05:32 as read
  • Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Giovanni Grazioso, Andrea Cavalli, Marco De Amici, Maurizio Recanatini, Carlo De Micheli
    posted to solvation protein-ligand_interactions electrostatics apbs by sobolevnrm to the group baker-group on 2008-06-30 11:30:07 as read
  • Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson-Boltzmann Equation
    J. Phys. Chem. B, Vol. 101, No. 7. (13 February 1997), pp. 1190-1197.
    by SR Edinger, C Cortis, PS Shenkin, RA Friesner
    posted to solvation electrostatics by sobolevnrm to the group baker-group on 2008-06-29 21:20:51 as read
  • Self-Consistent-Field Calculation of Pauli Repulsion and Dispersion Contributions to the Solvation Free Energy in the Polarizable Continuum Model
    J. Phys. Chem. B, Vol. 101, No. 6. (6 February 1997), pp. 1051-1057.
    by C Amovilli, B Mennucci
    posted to solvation quantum_mechanics nonpolar by sobolevnrm to the group baker-group on 2008-06-29 21:17:39 as read
  • Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics
    The Journal of Chemical Physics, Vol. 125, No. 7. (2006)
    by Jerry B Abrams, Lula Rosso, Mark E Tuckerman
    posted to solvation molecular_simulation by sobolevnrm to the group baker-group on 2008-06-29 21:13:31 as read
  • Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: A density functional approach
    The Journal of Chemical Physics, Vol. 126, No. 5. (2007)
    by B Husowitz, V Talanquer
    posted to statistical_mechanics solvation by sobolevnrm to the group baker-group on 2008-06-29 20:27:59 as read
  • 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 to the group baker-group on 2008-06-27 18:08:01 as read along with 1 person RamuAnandakrishnan
  • 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 electrostatics by sobolevnrm to the group baker-group on 2008-06-27 12:08:04 as read
  • 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 to the group baker-group on 2008-06-27 12:06:38 as read
  • 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 to the group baker-group on 2008-06-27 11:54:41 as read
  • Hydration of ionic species studied by the reference interaction site model with a repulsive bridge correction
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Gennady N Chuev, Maxim V Fedorov, Sandro Chiodo, Nino Russo, Emilia Sicilia
    posted to statistical_mechanics solvation electrostatics by sobolevnrm to the group baker-group on 2008-06-17 12:05:08 as read
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