dfgreen's solvation [44 articles] Export

Recent papers added to dfgreen's library classified by the tag solvation. You can also see everyone's solvation.

	Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation [My Copy] Journal of the American Chemical Society, Vol. 115, No. 21. (1 October 1993), pp. 9620-9631. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Peter A. Kollmann posted to ab-initio charges interactions quantum-mechanics solvation by dfgreen on 2009-01-09 01:55:58 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response [My Copy] Journal of Computational Chemistry, Vol. 20, No. 5. (1999), pp. 499-510. by Richard H. Henchman, Jonathan W. Essex posted to ab-initio charges free-energy perturbation quantum-mechanics solvation by dfgreen on 2009-01-08 23:33:59 as
	Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations [My Copy] The Journal of Chemical Physics, Vol. 100, No. 12. (1994), pp. 9050-9063. by Dmitrii Beglov, Benoît Roux posted to dynamics molecular solvation by dfgreen on 2009-01-08 23:07:33 as along with 2 people dmitry_s_yershov jwagoner
	Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis [My Copy] Proteins: Structure, Function, and Genetics, Vol. 4, No. 1. (1988), pp. 7-18. by Michael K. Gilson, Barry Honig posted to binding electrostatics poisson-boltzmann solvation by dfgreen on 2009-01-08 22:50:19 as along with 1 person flbarroso
	Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation [My Copy] The Journal of Physical Chemistry, Vol. 94, No. 19. (1990), pp. 7684-7692. by Kim A. Sharp, Barry Honig posted to electrostatics poisson-boltzmann solvation by dfgreen on 2009-01-08 22:46:01 as along with 2 people Elena_Zubova dmitry_s_yershov
	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 electrostatics poisson-boltzmann solvation by dfgreen on 2009-01-08 22:45:17 as along with 4 people melo_mcr onufriev dmitry_s_yershov flbarroso
	Molecular volume, surface area, and curvature dependence of the configurational entropy change upon solvation: effects of molecular bonding [My Copy] Chemical Physics Letters, Vol. 284, No. 3-4. (27 February 1998), pp. 235-246. by S. Shimizu, M. Ikeguchi, S. Nakamura, K. Shimizu posted to hydrophobic solvation by dfgreen on 2009-01-08 22:19:25 as along with 1 person sunrise
	Solvation of large molecules: Some exact results on the dependence on volume and surface area of the solute [My Copy] Biophysical Chemistry, Vol. 51, No. 2-3. (August 1994), pp. 203-216. by A. Bennaim posted to hydrophobic solvation by dfgreen on 2009-01-08 22:05:49 as
	Generalized born model with a simple smoothing function [My Copy] Journal of Computational Chemistry, Vol. 24, No. 14. (15 November 2003), pp. 1691-1702. by Wonpil Im, Michael S. Lee, Charles L. Brooks posted to electrostatics generalized-born solvation by dfgreen on 2009-01-08 21:58:20 as along with 3 people ckmyo stephenbond onufriev
	Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field [My Copy] Journal of the American Chemical Society, Vol. 128, No. 11. (1 March 2006), pp. 3728-3736. by Jianhan Chen, Wonpil Im, Charles L. Brooks posted to force-fields generalized-born interactions solvation by dfgreen on 2009-01-08 21:57:21 as along with 5 people ckmyo oteri yxue onufriev bilab
	One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. [My Copy] Protein science : a publication of the Protein Society, Vol. 14, No. 5. (May 2005), pp. 1293-1304. by S. A. Marshall, C. L. Vizcarra, S. L. Mayo posted to design electrostatics protein solvation by dfgreen on 2009-01-08 21:21:08 as
	Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects [My Copy] Science, Vol. 252, No. 5002. (5 April 1991), pp. 106-109. by K. A. Sharp, A. Nicholls, R. F. Fine, B. Honig posted to hydrophobic solvation by dfgreen on 2009-01-08 21:04:11 as along with 1 person softsimu
	Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution [My Copy] Journal of Solution Chemistry, Vol. 10, No. 8. (1981), pp. 563-595. by Sergio Cabani, Paolo Gianni, Vincenzo Mollica, Luciano Lepori posted to solvation by dfgreen on 2009-01-08 20:55:04 as
	Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields [My Copy] Journal of Computational Chemistry, Vol. 19, No. 7. (1998), pp. 769-780. by Rami M. Reddy, Mark D. Erion, Atul Agarwal, Vellarkad N. Viswanadhan, Quentin D. Mcdonald, Clark W. Still posted to charges electrostatics force-fields generalized-born solvation by dfgreen on 2009-01-08 20:50:07 as along with 1 person mijam
	Semianalytical treatment of solvation for molecular mechanics and dynamics [My Copy] Journal of the American Chemical Society, Vol. 112, No. 16. (1 August 1990), pp. 6127-6129. by W. Clark Still, Anna Tempczyk, Ronald C. Hawley, Thomas Hendrickson posted to electrostatics generalized-born solvation by dfgreen on 2009-01-08 20:48:38 as along with 6 people chemrahul82 blackgen Lombardo_7 GermanErlenkamp dmitry_s_yershov stephenbond
	The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii [My Copy] The Journal of Physical Chemistry A, Vol. 101, No. 16. (1 April 1997), pp. 3005-3014. by Di Qiu, Peter S. Shenkin, Frank P. Hollinger, W. Clark Still posted to electrostatics generalized-born solvation by dfgreen on 2009-01-08 20:46:08 as along with 4 people chemrahul82 GermanErlenkamp mijam jwagoner
	Partitioning of nonpolar solutes into bilayers and amorphous n-alkanes [My Copy] The Journal of Physical Chemistry, Vol. 94, No. 2. (1 January 1990), pp. 801-809. by Linda R. De Young, Ken A. Dill posted to hydrophobic solvation by dfgreen on 2009-01-08 20:45:13 as
	Solvation: Effects of molecular size and shape [My Copy] The Journal of Chemical Physics, Vol. 101, No. 8. (1994), pp. 7007-7026. by Hue S. Chan, Ken A. Dill posted to hydrophobic solvation by dfgreen on 2009-01-08 20:44:03 as
	On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models [My Copy] The Journal of Chemical Physics, Vol. 109, No. 12. (1998), pp. 4864-4872. by Nobuyuki Matubayasi, Emilio Gallicchio, Ronald M. Levy posted to hydrophobic solvation by dfgreen on 2009-01-08 20:42:49 as
	The Mechanism of Hydrophobic Solvation Depends on Solute Radius [My Copy] J. Phys. Chem. B, Vol. 104, No. 6. (17 February 2000), pp. 1326-1331. by N. T. Southall, K. A. Dill posted to hydrophobic solvation by dfgreen on 2009-01-08 20:40:17 as along with 2 people sunrise softsimu
	Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 9. (1 March 1995), pp. 2885-2892. by A. Wallqvist, B. J. Berne posted to dynamics hydrophobic molecular solvation by dfgreen on 2009-01-08 20:39:24 as
	Modeling hydrophobic solvation of nonspherical systems: Comparison of use of molecular surface area with accessible surface area [My Copy] Journal of Computational Chemistry, Vol. 18, No. 1. (1997), pp. 115-125. by Robert B. Hermann posted to hydrophobic solvation by dfgreen on 2009-01-08 20:37:56 as
	AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. [My Copy] Journal of computational chemistry, Vol. 25, No. 4. (March 2004), pp. 479-499. by E. Gallicchio, R. M. Levy posted to continuum-vdw generalized-born solvation by dfgreen on 2009-01-08 20:36:29 as along with 6 people flbarroso melo_mcr aphou RamuAnandakrishnan jwagoner onufriev
	Entropic Contributions to Free Energies of Solvation [My Copy] The Journal of Physical Chemistry, Vol. 98, No. 15. (1 April 1994), pp. 4141-4147. by David J. Giesen, Christopher J. Cramer, Donald G. Truhlar posted to hydrophobic solvation by dfgreen on 2009-01-08 20:27:01 as
	On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. [My Copy] Journal of the American Chemical Society, Vol. 125, No. 31. (6 August 2003), pp. 9523-9530. by R. M. Levy, L. Y. Zhang, E. Gallicchio, A. K. Felts posted to continuum-vdw hydrophobic solvation by dfgreen on 2009-01-08 20:21:20 as along with 1 person flbarroso
	Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 1. (1 January 2006), pp. 128-139. by Robert C. Rizzo, Tiba Aynechi, David A. Case, Irwin D. Kuntz posted to charges electrostatics generalized-born hydrophobic solvation by dfgreen on 2009-01-08 20:18:55 as
	Optimized Radii for Poisson−Boltzmann Calculations with the AMBER Force Field [My Copy] Journal of Chemical Theory and Computation, Vol. 1, No. 3. (1 May 2005), pp. 484-493. by Jessica M. Swanson, Stewart A. Adcock, Andrew J. Mccammon posted to electrostatics force-fields solvation by dfgreen on 2009-01-08 20:17:34 as
	Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions [My Copy] The Journal of Physical Chemistry, Vol. 96, No. 15. (1 July 1992), pp. 6428-6431. by V. Mohan, M. E. Davis, J. A. Mccammon, B. M. Pettitt posted to electrostatics solvation by dfgreen on 2009-01-08 20:13:46 as
	Accuracy of free energies of hydration for organic molecules from 6-31g-derived partial charges [My Copy] Journal of Computational Chemistry*, Vol. 14, No. 10. (1993), pp. 1240-1249. by Heather A. Carlson, Toan B. Nguyen, Modesto Orozco, William L. Jorgensen posted to ab-initio charges quantum-mechanics solvation by dfgreen on 2009-01-08 20:10:28 as along with 1 person allmensch
	Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory [My Copy] Journal of the American Chemical Society, Vol. 116, No. 26. (1 December 1994), pp. 11875-11882. by David J. Tannor, Bryan Marten, Robert Murphy, et al.Richard A. Friesner, Doree Sitkoff, Anthony Nicholls, Barry Honig, Murco Ringnalda, William A. Goddard posted to ab-initio charges electrostatics quantum-mechanics solvation by dfgreen on 2009-01-08 19:55:29 as
	Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 29. (1 July 1995), pp. 11575-11583. by Yanbo Ding, Dan N. Bernardo, Karsten Krogh-Jespersen, Ronald M. Levy posted to dynamics free-energy molecular perturbation solvation by dfgreen on 2009-01-08 19:54:00 as
	New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 28. (1 January 1996), pp. 11775-11788. by Bryan Marten, Kyungsun Kim, Christian Cortis, et al.Richard A. Friesner, Robert B. Murphy, Murco N. Ringnalda, Doree Sitkoff, Barry Honig posted to ab-initio electrostatics quantum-mechanics solvation by dfgreen on 2009-01-08 19:52:17 as
	Solvation Free Energies of Amides and Amines: Disagreement between Free Energy Calculations and Experiment [My Copy] Journal of the American Chemical Society, Vol. 117, No. 22. (1 June 1995), pp. 6057-6063. by Pierre-Yves Morgantini, Peter A. Kollman posted to free-energy perturbation solvation by dfgreen on 2009-01-08 19:39:58 as
	Investigating the Anomalous Solvation Free Energies of Amines with a Polarizable Potential [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 6. (1 January 1996), pp. 2367-2371. by Elaine C. Meng, James W. Caldwell, Peter A. Kollman posted to force-fields solvation by dfgreen on 2009-01-08 19:36:19 as
	OPLS All-Atom Model for Amines: Resolution of the Amine Hydration Problem [My Copy] Journal of the American Chemical Society, Vol. 121, No. 20. (1 May 1999), pp. 4827-4836. by Robert C. Rizzo, William L. Jorgensen posted to solvation by dfgreen on 2009-01-08 19:23:02 as
	Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants. [My Copy] J Comput Aided Mol Des, Vol. 15, No. 8. (August 2001), pp. 721-740. by J. Mendes, A. M. Baptista, M. A. Carrondo, C. M. Soares posted to design mean-field protein solvation stability by dfgreen on 2009-01-08 18:35:31 as along with 1 person and 1 group nknii TCR_Signaling
	Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 101, No. 26. (1 June 1997), pp. 5239-5248. by Mafalda Nina, Dmitri Beglov, Benoit Roux posted to electrostatics free-energy perturbation solvation by dfgreen on 2009-01-08 17:46:14 as along with 3 people ckmyo dmitry_s_yershov stephenbond
	Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. [My Copy] Protein science : a publication of the Protein Society, Vol. 13, No. 4. (April 2004), pp. 925-936. by N. Pokala, T. M. Handel posted to design electrostatics protein solvation by dfgreen on 2009-01-08 17:44:52 as
	Effective scoring function for protein sequence design. [My Copy] Proteins, Vol. 54, No. 2. (1 February 2004), pp. 271-281. by S. Liang, N. V. Grishin posted to design protein solvation by dfgreen on 2009-01-08 17:42:30 as
	Tanford-Kirkwood electrostatics for protein modeling. [My Copy] Proc Natl Acad Sci U S A, Vol. 96, No. 20. (28 September 1999), pp. 11145-11150. by J. J. Havranek, P. B. Harbury posted to electrostatics solvation by dfgreen on 2009-01-08 14:06:36 as along with 2 people onufriev dimka
	Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids [My Copy] The Journal of Physical Chemistry B, Vol. 106, No. 42. (1 October 2002), pp. 11026-11035. by Nilesh K. Banavali, Benoıt Roux posted to dna electrostatics rna solvation by dfgreen on 2009-01-08 13:00:47 as
	Pairwise calculation of protein solvent-accessible surface areas. [My Copy] Folding & design, Vol. 3, No. 4. (1998), pp. 253-258. by A. G. Street, S. L. Mayo posted to design protein solvation by dfgreen on 2009-01-08 12:56:10 as along with 1 person hryk
	Evaluation of ab Initio Charge Determination Methods for Use in Continuum Solvation Calculations [My Copy] J. Phys. Chem. B, Vol. 107, No. 37. (18 September 2003), pp. 10261-10273. by D. F. Green, B. Tidor posted to ab-initio charges electrostatics quantum-mechanics solvation by dfgreen on 2009-01-07 20:39:07 as along with 1 person loison
	Solvation thermodynamics of amino acids [My Copy] Journal of the Chemical Society, Faraday Transactions, Vol. 93 (1997), pp. 1105-1113. by Surjit B. Dixit, R. Bhasin, E. Rajasekaran, B. Jayaram posted to solvation by dfgreen on 2009-01-07 18:52:24 as

Note: You may cite this page as: http://www.citeulike.org/user/dfgreen/tag/solvation

file-import-09-01-07b	274
electrostatics	96
protein	90
design	63
dynamics	47
molecular	47
ligand	46
solvation	44
binding	39
packing	19
quantum-mechanics	19
charges	18
optimization	18
free-energy	17
interactions	17
pka	17
review	17
perturbation	16
ab-initio	15
force-fields	15
generalized-born	13
hydrophobic	13
engineering	11
protein-protein	11
software	11
specificity	9
stability	9
poisson-boltzmann	7
structure	7
biopharmaceuticals	6
carbohydrate	6
conformational	6
docking	5
enzyme	5
biology	4
catalysis	4
dna	4
homology	4
preferences	4
sequence	4
systems	4
entropy	3
kinetics	3
linear-programming	3
quadratic-programming	3
semi-empirical	3
continuum-vdw	2
monte-carlo	2
protonation	2
rna	2
structure-prediction	2
visualization	2
water	2
action-at-a-distance	1
allostery	1
analysis	1
atp	1
brownian	1
calmodulin	1
dissociation	1
effect	1
electrochemistry	1
folding	1
g-protein	1
harmonics	1
hierarchicies	1
mean-field	1
membrane-association	1
phylogeny	1
proteomics	1
resistance	1
rna-protein	1
senstivity	1
text	1
vibrational	1

dfgreen's solvation [44 articles] Export

dfgreen's tags