Tag solvation [at least 200 articles] Export

Recent papers classified by the tag solvation.

	Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 204-216. by Alexey K. Shaytan, Victor A. Ivanov, Konstantin V. Shaitan, Alexei R. Khokhlov posted to solvation pmf free-energy forcefield by agrossfield on 2009-11-24 13:57:39 as
	Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 43. (29 October 2009), pp. 14343-14354. by Zunnan Huang, Chung F. Wong posted to solvation protein_dynamics protein-ligand peptides molecular_dynamics_simulations md_simulation drug-discovery conformational_transitions binding by jmccammon to the group McCammon on 2009-11-21 20:27:49 as along with 1 person anuragsethi
	Difference of solvation site between halide ions and electrons in an alkylammonium ionic liquid [My Copy] Chemical Physics Letters, Vol. 482, No. 4-6. (12 November 2009), pp. 259-262. by Ryuzi Katoh posted to solvation rtil alkylamm by majdula on 2009-11-06 16:04:08 as
	Toward a Unified Representation of Protein Structural Dynamics in Solution [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Phineus R. L. Markwick, Guillaume Bouvignies, Loic Salmon, J. Andrew McCammon, Michael Nilges, Martin Blackledge posted to solvation protein_flexibility nov09 nmr jacs dynamics by klexa on 2009-11-04 15:41:26 as
	Enhanced surface hydrophobicity by coupling of surface polarity and topography [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 36. (8 September 2009), pp. 15181-15185. by Nicolas Giovambattista, Pablo G. Debenedetti, Peter J. Rossky posted to solvation nonpolar electrostatics by sobolevnrm on 2009-10-31 00:58:41 as
	Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 36. (8 September 2009), pp. 15119-15124. by Rahul Godawat, Sumanth N. Jamadagni, Shekhar Garde posted to solvation nonpolar by sobolevnrm on 2009-10-31 00:58:33 as along with 1 person softsimu
	Ion distribution around a charged rod in one and two component solvents: Preferential solvation and first order ionization phase transition [My Copy] The Journal of Chemical Physics, Vol. 131, No. 9. (2009), 094905. by Ryuichi Okamoto, Akira Onuki posted to statistical_mechanics solvation electrostatics by sobolevnrm on 2009-10-31 00:37:11 as
	Parameterization and Validation of Solvation Corrected Atomic Radii† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 43. (29 October 2009), pp. 12028-12034. by Chun-Shan Zuo, Olaf Wiest, Yun-Dong Wu posted to solvation electrostatics by sobolevnrm on 2009-10-31 00:15:11 as
	Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2583-2588. by Wei Jiang, Milan Hodoscek, Benoît Roux posted to solvation molecular_simulation electrostatics by sobolevnrm on 2009-10-31 00:09:30 as along with 1 person qshao
	Hydrophobic Interactions of Hexane in Nanosized Water Droplets [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 36. (10 September 2009), pp. 12337-12342. by Dirar Homouz, Byron Hoffman, Margaret S. Cheung posted to solvation nonpolar by sobolevnrm on 2009-10-27 11:40:02 as
	Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins [My Copy] J. Gen. Physiol., Vol. 129, No. 5. (30 April 2007), pp. 357-362. by Richard Wolfenden posted to solvation parameters aminoacids by melo_mcr on 2009-10-27 00:41:43 as along with 1 person ashaytan
	Entropic trends in aqueous solutions of the common functional groups [My Copy] Faraday Discuss. (2010) by Sheeba J. Irudayam, Richard D. Plumb, Richard H. Henchman posted to statistical_mechanics solvation by sobolevnrm on 2009-10-24 22:41:48 as
	Affinities of amino acid side chains for solvent water [My Copy] Biochemistry, Vol. 20, No. 4. (1 February 1981), pp. 849-855. by R. Wolfenden, L. Andersson, P. M. Cullis, C. C. B. Southgate posted to solvation parameters aminoacids by melo_mcr on 2009-10-23 21:01:32 as
	Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models [My Copy] The Journal of Physical Chemistry, Vol. 98, No. 7. (1 February 1994), pp. 1978-1988. by Doree Sitkoff, Kim A. Sharp, Barry Honig posted to solvation parameters aminoacids by melo_mcr on 2009-10-23 20:59:47 as along with 4 people onufriev dmitry_s_yershov flbarroso dfgreen
	Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution [My Copy] Biochemistry, Vol. 27, No. 5. (1 March 1988), pp. 1664-1670. by Anna Radzicka, Richard Wolfenden posted to solvation parameters aminoacids by melo_mcr on 2009-10-23 20:58:22 as
	Differentiation of lipid-associating helices by use of three-dimensional molecular hydrophobicity potential calculations. [My Copy] Journal of Biological Chemistry, Vol. 266, No. 24. (25 August 1991), pp. 16120-16127. by R. Brasseur posted to solvation parameters folding energy_function by melo_mcr on 2009-10-17 21:46:34 as
	Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex [My Copy] Journal of Computational Chemistry, Vol. 18, No. 6. (1997), pp. 723-743. by Amedeo Caflisch, Stefan Fischer, Martin Karplus posted to solvation protein_surface energy_function by melo_mcr on 2009-10-17 21:12:04 as along with 1 person flbarroso
	The impact of monovalent ion force field model in nucleic acids simulations [My Copy] Phys. Chem. Chem. Phys. (2009) by Agnes Noy, Ignacio Soteras, F. Javier Luque, Modesto Orozco posted to solvation review nucleic_acids electrostatics by sobolevnrm on 2009-10-17 01:34:55 as
	Assessing the performance of implicit solvation models at a nucleic acid surface [My Copy] Phys. Chem. Chem. Phys., Vol. 10, No. 32. (2008), pp. 4889-4902. by Feng Dong, Jason A. Wagoner, Nathan A. Baker posted to solvation nucleic_acids molecular_simulation electrostatics by sobolevnrm on 2009-10-16 13:35:01 as along with 3 people and 1 group onufriev simone jmccammon McCammon
	Universal Solvation Model Based on the Generalized Born Approximation with Asymmetric Descreening [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2447-2464. by Aleksandr V. Marenich, Christopher J. Cramer, Donald G. Truhlar posted to solvation electrostatics by sobolevnrm on 2009-10-15 12:33:33 as along with 2 people RamuAnandakrishnan acpan
	Three-dimensional “Mercedes-Benz” model for water [My Copy] The Journal of Chemical Physics, Vol. 131, No. 5. (2009), 054505. by Cristiano L. Dias, Tapio A. Nissila, Martin Grant, Mikko Karttunen posted to solvation by sobolevnrm on 2009-10-14 12:27:59 as along with 2 people softsimu dlimmer
	Towards a first principles prediction of p<i>K</i><sub>a</sub>: COSMO-RS and the cluster-continuum approach [My Copy] Molecular Physics: An International Journal at the Interface Between Chemistry and Physics (2009) by Frank Eckert, Michael Diedenhofen, Andreas Klamt posted to solvation quantum_chemistry pka by flbarroso on 2009-10-13 20:28:43 as
	Prediction of the Water Content in Protein Binding Sites [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13337-13346. by Julien Michel, Julian Tirado-Rives, William L. Jorgensen posted to water_molecules solvation simulation_methodology protein-ligand monte_carlo md_simulation free_energy drug-discovery binding by jmccammon to the group McCammon on 2009-10-10 21:07:02 as along with 2 people snichols15 qshao
	The AGBNP2 Implicit Solvation Model [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2544-2564. by Emilio Gallicchio, Kristina Paris, Ronald M. Levy posted to solvation nonpolar electrostatics by sobolevnrm on 2009-10-01 13:14:35 as
	Entropy crossover from molecular to macroscopic cavity hydration [My Copy] Chemical Physics Letters, Vol. 477, No. 1-3. (28 July 2009), pp. 109-111. by Henry S. Ashbaugh posted to solvation nonpolar by sobolevnrm on 2009-10-01 13:14:10 as
	Wavelet BEM on molecular surfaces: parametrization and implementation [My Copy] Computing, Vol. 86, No. 1. (1 September 2009), pp. 1-22. by Helmut Harbrecht, Maharavo Randrianarivony posted to solvation mathematics electrostatics boundary_element by sobolevnrm on 2009-10-01 13:13:49 as
	Optimal docking area: a new method for predicting protein-protein interaction sites. [My Copy] Proteins, Vol. 58, No. 1. (1 January 2005), pp. 134-143. by J. Fernandez-Recio, M. Totrov, C. Skorodumov, R. Abagyan posted to structural_model solvation protein-protein protein-ligand docking 2005 by klexa on 2009-09-29 20:57:02 as along with 5 people and 2 groups jwm bicko schlauchi cjeans marti Radiation_Damage Stressosome
	Do Structurally Similar Ligands Bind in a Similar Fashion? [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 23. (1 November 2006), pp. 6716-6725. by Jonas Bostrom, Anders Hogner, Stefan Schmitt posted to solvation similiarity side-chain sbdd protein_flexibility ligand flexibility drug_discovery 2006 by klexa on 2009-09-29 20:45:59 as along with 4 people schlauchi daevans superpyrin nickolay
	Amino acid chemistry in dipolar aprotic solvents: dissociation constants and ambident reactivity [My Copy] The Journal of Organic Chemistry, Vol. 51, No. 13. (1 June 1986), pp. 2579-2585. by David L. Hughes, James J. Bergan, Edward J. J. Grabowski posted to solvation paper1 hydration amino_acid_chemistry by whitead to the group Jiang Research Group on 2009-09-09 23:20:55 as
	Effects of solvents on the tautomerization of <I>N,N-</I>dimethylglycine [My Copy] Journal of Physical Organic Chemistry, Vol. 10, No. 12. (1997), pp. 898-900. by Allan D. Headley, Rita E. Corona, Eric T. Cheung posted to solvation paper1 hydration dmg by whitead to the group Jiang Research Group on 2009-09-09 23:06:17 as
	Dimerization Thermodynamics of Large Hydrophobic Plates: A Scaled Particle Theory Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 32. (13 August 2009), pp. 11232-11239. by Giuseppe Graziano posted to solvation nonpolar by sobolevnrm on 2009-09-01 12:44:03 as
	How Well Does Poisson−Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 37. (1 September 2006), pp. 18680-18687. by Chunhu Tan, Lijiang Yang, Ray Luo posted to solvation pb continnum by flbarroso on 2009-08-24 21:40:06 as along with 1 person and 1 group sobolevnrm baker-group
	The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation [My Copy] The Journal of Chemical Physics, Vol. 131, No. 3. (2009), 034102. by Avisek Das, Hans C. Andersen posted to statistical_mechanics solvation nonpolar multiscale by sobolevnrm on 2009-08-19 12:55:48 as along with 3 people tomweingarten dlimmer agrossfield
	How to obtain statistically converged MM/GBSA results [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Samuel Genheden, Ulf Ryde posted to solvation molecular_simulation free_energy electrostatics by sobolevnrm on 2009-08-19 12:54:22 as along with 3 people and 1 group pmung barry RamuAnandakrishnan McCammon
	Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins [My Copy] Nat Struct Mol Biol, Vol. 16, No. 7. (14 July 2009), pp. 684-690. by Jianmin Gao, Daryl A. Bosco, Evan T. Powers, Jeffery W. Kelly posted to structure solvation protein_folding nonpolar electrostatics by sobolevnrm on 2009-08-18 12:37:06 as along with 1 person and 2 groups barry structural_bioinformatics McCammon
	A simple polarizable model of water based on classical Drude oscillators [My Copy] The Journal of Chemical Physics, Vol. 119, No. 10. (2003), pp. 5185-5197. by Guillaume Lamoureux, Jr, Benoît Roux posted to solvation polarization by afenley on 2009-08-15 22:58:17 as
	On the Number of Water Molecules Necessary To Stabilize the Glycine Zwitterion [My Copy] Journal of the American Chemical Society, Vol. 117, No. 31. (1 August 1995), pp. 8159-8170. by Jan H. Jensen, Mark S. Gordon posted to water structure solvation quantum paper1 glycine by whitead to the group Jiang Research Group on 2009-08-14 17:23:11 as
	NaCl-dependent formation of the highly crystalline phase in sufficiently hydrated dimyristoylphosphatidylglycerol bilayers [My Copy] Chemistry and Physics of Lipids, Vol. 161, No. 1. (01 September 2009), pp. 1-10. by Masanao Kinoshita, Satoru Kato, Hiroshi Takahashi posted to solvation electrostatics biomembranes by sobolevnrm on 2009-08-13 13:27:26 as
	Ion-blocking sites of the Kir2.1 channel revealed by multiscale modeling [My Copy] Biochemistry, Vol. 0, No. ja. (0000) by Kaihsu Tai, Phillip J. Stansfeld, Mark S. P. Sansom posted to solvation ion_channels electrostatics biomembranes by sobolevnrm on 2009-08-13 13:27:11 as
	P<FONT SIZE='-2'>ACKMOL</FONT>: A package for building initial configurations for molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2157-2164. by L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez posted to solvation software molecular_dynamics jcc aug09 by klexa on 2009-08-11 19:50:10 as along with 2 people and 1 group whitead middledomain Jiang Research Group
	Protein Hydration Dynamics and Molecular Mechanism of Coupled Water−Protein Fluctuations [My Copy] Journal of the American Chemical Society, Vol. 131, No. 30. (5 August 2009), pp. 10677-10691. by Luyuan Zhang, Yi Yang, Ya-Ting Kao, Lijuan Wang, Dongping Zhong posted to kinetics solvation by sobolevnrm on 2009-08-10 13:01:38 as along with 2 people kjell marissalee
	Variable atomic radii for continuum-solvent electrostatics calculation. [My Copy] The Journal of chemical physics, Vol. 129, No. 1. (7 July 2008) by Baojing Zhou, Manish Agarwal, Chung F. Wong posted to atomic radii solvation by superpyrin on 2009-08-04 10:43:06 as along with 1 person onufriev
	Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10255-10260. by Jens Carlsson, Johan Åqvist posted to molecular_dynamics solvation by sobolevnrm on 2009-08-03 21:17:12 as along with 2 people francescamocci carlosjavierna
	Characterization of Water Wires inside Hydrophobic Tubular Peptide Structures [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Upadhyayula S. Raghavender, Subrayashastry Aravinda, Narayanaswamy Shamala, Kantharaju, Rajkishor Rai, Padmanabhan Balaram posted to nonpolar solvation thrombin by sobolevnrm on 2009-08-03 21:17:05 as
	The impact of hydration water on the dynamics of side chains of hydrophobic peptides: From dry powder to highly concentrated solutions [My Copy] The Journal of Chemical Physics, Vol. 130, No. 23. (2009), 235101. by Daniela Russo, José Teixeira, Jacques Ollivier posted to kinetics molecular_dynamics solvation by sobolevnrm on 2009-08-03 21:16:50 as
	Chapter 9 Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting [My Copy] Methods in enzymology In Computer Methods, Part A, Vol. 454 (2009), pp. 233-258. by Jens E. Nielsen posted to drug-discovery electrostatics protein-ligand solvation by jmccammon to the group McCammon on 2009-07-27 19:09:08 as along with 4 people and 1 group sobolevnrm scampos anuragsethi flbarroso baker-group
	Polarization effects in molecular mechanical force fields [My Copy] Journal of Physics: Condensed Matter, Vol. 21, No. 33. (2009), 333102. by Piotr Cieplak, Francois-Yves Dupradeau, Yong Duan, Junmei Wang posted to electrostatics md_simulation solvation by jmccammon to the group McCammon on 2009-07-27 18:02:24 as along with 1 person anuragsethi
	Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent [My Copy] Chemical Reviews, Vol. 94, No. 7. (1 November 1994), pp. 2027-2094. by Jacopo Tomasi, Maurizio Persico posted to continnum solvation by flbarroso on 2009-07-25 22:24:38 as
	Quantum Mechanical Continuum Solvation Models [My Copy] Chemical Reviews, Vol. 105, No. 8. (1 August 2005), pp. 2999-3094. by Jacopo Tomasi, Benedetta Mennucci, Roberto Cammi posted to continnum solvation by flbarroso on 2009-07-25 22:22:57 as along with 2 people and 1 group whitead ucbcjbm Jiang Research Group
	Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. [My Copy] Journal of molecular biology, Vol. 390, No. 4. (24 July 2009), pp. 805-819. by Alan A. Chen, David E. Draper, Rohit V. Pappu posted to electrostatics nucleic_acids solvation by sobolevnrm on 2009-07-23 13:11:38 as

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electrostatics	628
biomembranes	149
statistical_mechanics	138
molecular_simulation	136
pka	102
nonpolar	92
nucleic_acids	70
molecular_dynamics	60
diffusion	44
water	43
protein-ligand_interactions	40
free_energy	39
mathematics	37
multiscale	35
kinetics	34
protein_folding	33
integral_equation	32
experimental_methodology	30
beyond_mean_field	29
review	29
structure	29
md_simulation	26
protein-ligand	23
ion_channels	21
interfaces	20
protein-protein_interactions	20
binding	19
hydrophobic	19
continnum	18
quantum_mechanics	18
drug-discovery	15
software	15
theory	15
dynamics	14
nanotech	14
protein	14
protein-nucleic_acid_interactions	14
docking	13
hydration	13
geometry	11
hydrophobicity	11
apbs	10
implicit	10
bioinformatics	9
generalized-born	9
protein-protein	9
simulations	9
free-energy	8
nmr	8
thrombin	8
aminoacids	7
charges	7
fee	7
force-fields	7
forcefield	7
monte_carlo	7
paper1	7
protein-membrane_interactions	7
ab-initio	6
born	6
drug_design	6
femtosecond	6
md	6
molecular	6
peptide	6
programming	6
quantum-mechanics	6
visualization	6
design	5
experiment	5
ions	5
mechanics	5
parameters	5
poisson-boltzmann	5
allostery	4
glycine	4
interface	4
ion	4
ligand-membrane_interactions	4
lin	4
modeling	4
pb	4
pdb2pqr	4
peptides	4
perturbation	4
protein_dynamics	4
protein_engineering	4
quantum	4
simulation	4
additivity	3
atomic	3
electrostatic	3
hydrogen	3
hyperpolarizability	3
prediction	3
protein_dna	3
protein_flexibility	3
screening	3
simulation_methodology	3
solution	3

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