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	Free Energy of Solvation, Interaction, and Binding of Arbitrary Charge Distributions Imbedded in a Dielectric Continuum [My Copy] The Journal of Physical Chemistry, Vol. 98, No. 22. (1 June 1994), pp. 5773-5777. by B. Jayaram posted to ions implicit_solvation by onufriev on 2009-12-23 08:08:35 as
	A comparison of generalized Born methods in folding simulations [My Copy] Chemical Physics Letters, Vol. 460, No. 1-3. (20 July 2008), pp. 295-299. by Tohru Terada,, Kentaro Shimizu, posted to implicit_solvation gb by boris_aguilar on 2009-12-12 00:49:34 as
	Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor [My Copy] Journal of Computational Chemistry, Vol. 29, No. 11. (2008), pp. 1707-1724. by Michel Masella, Daniel Borgis, Philippe Cuniasse posted to implicit_solvation coarse_grain by boris_aguilar on 2009-11-05 22:14:29 as along with 2 people middledomain sunhwan
	On Finite-Size Corrections to the Free Energy of Ionic Hydration [My Copy] The Journal of Physical Chemistry B, Vol. 101, No. 29. (1 July 1997), pp. 5622-5623. by Francisco Figueirido, Gabriela S. Del Buono, Ronald M. Levy posted to molecular_dynamics implicit_solvation by onufriev on 2009-10-30 03:22:38 as
	Free Energy of Ionic Hydration [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 4. (1 January 1996), pp. 1206-1215. by Gerhard Hummer, Lawrence R. Pratt, Angel E. Garcia posted to water_molecules ions implicit_solvation charge_asymmetry by onufriev on 2009-10-30 03:19:05 as
	A Comprehensive Analytical Treatment of Continuum Electrostatics [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 5. (1 January 1996), pp. 1578-1599. by Michael Schaefer, Martin Karplus posted to implicit_solvation analytical_electrostatics by boris_aguilar on 2009-10-27 22:12:46 as along with 1 person dfgreen
	Steric Effects in Electrolytes: A Modified Poisson-Boltzmann Equation [My Copy] Physical Review Letters, Vol. 79, No. 3. (21 Jul 1997), pp. 435-438. by Itamar Borukhov, David Andelman, Henri Orland posted to implicit_solvation beyond_pb by onufriev on 2009-08-14 06:51:30 as
	Beyond the Poisson-Boltzmann Model: Modeling Biomolecule-Water and Water-Water Interactions [My Copy] Physical Review Letters, Vol. 102, No. 8. (2009), 087801. by Patrice Koehl, Henri Orland, Marc Delarue posted to implicit_solvation beyond_pb by onufriev on 2009-08-14 02:55:24 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Dipolar Poisson-Boltzmann Equation: Ions and Dipoles Close to Charge Interfaces [My Copy] Physical Review Letters, Vol. 99, No. 7. (2007), 077801. by Ariel Abrashkin, David Andelman, Henri Orland posted to implicit_solvation beyond_pb by onufriev on 2009-08-13 23:30:00 as along with 1 person and 1 group sobolevnrm baker-group
	A formally exact field theory for classical systems at equilibrium [My Copy] Journal of Physics A: Mathematical and Theoretical, Vol. 41, No. 12. (2008), 125401. by Di D. Caprio, J. P. Badiali posted to implicit_solvation beyond_pb by onufriev on 2009-08-13 23:15:09 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 pb implicit_solvation by onufriev on 2009-08-13 23:10:21 as along with 3 people and 1 group sobolevnrm simone jmccammon McCammon
	Beyond Poisson-Boltzmann: Fluctuation effects and correlation functions [My Copy] The European Physical Journal E: Soft Matter and Biological Physics, Vol. 1, No. 2. (19 February 2000), pp. 203-214. by R. R. Netz, H. Orland posted to pb implicit_solvation beyond_pb by onufriev on 2009-08-13 23:02:31 as along with 1 person sobolevnrm
	Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 22. (30 May 2006), pp. 8331-8336. by Jason A. Wagoner, Nathan A. Baker posted to implicit_solvation nonpolar_molecules by afenley on 2009-07-22 19:46:00 as along with 3 people ahmetbakan flbarroso rok
	Application of the level-set method to the implicit solvation of nonpolar molecules [My Copy] The Journal of Chemical Physics, Vol. 127, No. 8. (2007), 084503. by Li T. Cheng, Joachim Dzubiella, J. Andrew Mccammon, Bo Li posted to implicit_solvation nonpolar_molecules by afenley on 2009-07-22 19:33:07 as along with 2 people and 2 groups csrocha sobolevnrm structural_bioinformatics baker-group
	Coupling Hydrophobicity, Dispersion, and Electrostatics in Continuum Solvent Models [My Copy] Physical Review Letters, Vol. 96, No. 8. (2006), 087802. by J. Dzubiella, J. M. J. Swanson, J. A. Mccammon posted to electrostatics hydrophobic implicit_solvation by afenley on 2009-07-22 19:29:34 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 implicit_solvation pb by onufriev on 2009-07-10 04:25:45 as along with 4 people melo_mcr dmitry_s_yershov flbarroso dfgreen
	Parameter Dependence in Continuum Electrostatic Calculations: A Study Using Protein Salt Bridges [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 22. (1 May 1998), pp. 4404-4410. by Zachary S. Hendsch, Charles V. Sindelar, Bruce Tidor posted to implicit_solvation pb by onufriev on 2009-07-10 04:17:32 as along with 1 person dfgreen
	Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 24. (18 June 2009), pp. 8206-8209. by Enrico O. Purisima, Traian Sulea posted to implicit_solvation electrostatics beyond_pb by onufriev on 2009-07-04 01:14:30 as along with 3 people and 1 group Elena_Zubova agrossfield sobolevnrm baker-group
	A Gaussian Description of Molecular Shape [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 11. (1 March 1995), pp. 3503-3510. by J. A. Grant, B. T. Pickup posted to gb implicit_solvation surface by onufriev on 2009-06-16 01:34:29 as along with 1 person sobolevnrm
	Electrostatic models in the theory of solutions [My Copy] J. Chem. Soc., Faraday Trans. 2, Vol. 72 (1976), pp. 361-371. by Yu Kharkats, A. A. Kornyshev, M. A. Vorotyntsev posted to electrostatics implicit_solvation by onufriev on 2009-06-16 01:16:46 as
	A test of implicit solvent models on the folding simulation of the GB1 peptide [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 195104. by Qiang Shao, Lijiang Yang, Yi Q. Gao posted to generalized_born implicit_solvation molecular_dynamics by afenley on 2009-05-22 23:09:47 as along with 1 person dlimmer
	Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 27, No. 6. (2006), pp. 719-729. by Jana Chocholouscaronová, Michael Feig posted to gb implicit_solvation molecular_dynamics by boris_aguilar on 2009-05-19 16:24:02 as along with 1 person yxue
	Generalized Born Model with a Simple, Robust Molecular Volume Correction [My Copy] J. Chem. Theory Comput., Vol. 3, No. 1. (9 January 2007), pp. 156-169. by J. Mongan, C. Simmerling, J. A. Mccammon, D. A. Case, A. Onufriev posted to gb implicit_solvation by boris_aguilar on 2009-05-16 05:08:59 as along with 1 person RamuAnandakrishnan
	Classical electrostatics in biology and chemistry. [My Copy] Science (New York, N.Y.), Vol. 268, No. 5214. (26 May 1995), pp. 1144-1149. by B. Honig, A. Nicholls posted to implicit_solvation pb by onufriev on 2009-05-02 07:23:47 as along with 5 people ckmyo dmitry_s_yershov stephenbond flbarroso apostola
	Continuum molecular electrostatics, salt effects, and counterion binding - A review of the Poisson-Boltzmann theory and its modifications [My Copy] Biopolymers, Vol. 89, No. 2. (February 2008), pp. 93-113. by Pawe&lstrok; Grochowski, Joanna Trylska posted to implicit_solvation pb by onufriev on 2009-05-02 07:17:38 as along with 7 people and 1 group loison melo_mcr krapnik flbarroso sobolevnrm softsimu mikaellund baker-group
	Folding of the Villin Headpiece Subdomain from Random Structures. Analysis of the Charge Distribution as a Function of pH [My Copy] Journal of Molecular Biology, Vol. 339, No. 4. (June 2004), pp. 915-925. by D. Ripoll posted to implicit_solvation ph protein_folding by onufriev on 2008-11-08 22:44:59 as
	Folding simulations of a three-stranded antiparallel β-sheet peptide [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 20. (2000), pp. 10780-10785. by Philippe Ferrara, Amedeo Caflisch posted to implicit_solvation protein_folding by onufriev on 2008-11-08 22:24:24 as along with 1 person doktornoe
	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 implicit_solvation pb by onufriev on 2008-10-09 00:43:04 as along with 1 person superpyrin
	Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics [My Copy] Biophys. J. (26 September 2008), biophysj.108.131649. by Cyril Azuara, Henri Orland, Michael Bon, Patrice Koehl, Marc Delarue posted to implicit_solvation beyond_pb by onufriev on 2008-10-09 00:41:16 as along with 3 people and 2 groups sobolevnrm oteri Elena_Zubova baker-group Structural Biology Group TorVergata
	Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions [My Copy] The Journal of Physical Chemistry A, Vol. 101, No. 43. (1 October 1997), pp. 8098-8106. by Marco Scarsi, Joannis Apostolakis, Amedeo Caflisch posted to gb implicit_solvation by onufriev on 2008-09-18 00:27:29 as along with 3 people flbarroso dmitry_s_yershov RamuAnandakrishnan
	An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis [My Copy] The Journal of Chemical Physics, Vol. 129, No. 7. (2008) by Andrew T. Fenley, John C. Gordon, Alexey Onufriev posted to electrostatics implicit_solvation poisson-boltzmann by afenley on 2008-09-17 20:50:21 as along with 2 people RamuAnandakrishnan agrossfield
	Implicit Solvent Electrostatics in Biomolecular Simulation [My Copy] New Algorithms for Macromolecular Simulation (2006), pp. 263-295. by Nathan Baker, Donald Bashford, David Case posted to gb implicit_solvation pb by onufriev on 2008-09-14 23:15:03 as along with 6 people flbarroso Scis0000002 dmitry_s_yershov stephenbond sunhwan qwermish
	Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models [My Copy] Journal of Computational Chemistry, Vol. 25, No. 13. (2004), pp. 1623-1629. by Jason Wagoner, Nathan A. Baker posted to implicit_solvation pb water_models by onufriev on 2008-09-14 20:52:11 as along with 2 people flbarroso qwermish
	Solvation of complex molecules in a polar liquid: An integral equation theory [My Copy] The Journal of Chemical Physics, Vol. 104, No. 21. (1996), pp. 8678-8689. by Dmitrii Beglov, Benoît Roux posted to electrostatics implicit_solvation water_models by onufriev on 2008-09-14 03:57:25 as along with 2 people dmitry_s_yershov stephenbond
	Computational sidechain placement and protein mutagenesis with implicit solvent models. [My Copy] Proteins, Vol. 67, No. 4. (1 June 2007), pp. 853-867. by A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis, T. Simonson posted to implicit_solvation protein_folding by onufriev on 2008-09-11 20:20:25 as along with 1 person msuarezdiez
	Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study [My Copy] Journal of Computational Chemistry, Vol. 24, No. 12. (2003), pp. 1432-1436. by Bojan Zagrovic, Vijay Pande posted to gb implicit_solvation protein_folding by onufriev on 2008-09-10 05:33:35 as
	Continuum polarizable force field within the Poisson-Boltzmann framework. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 25. (26 June 2008), pp. 7675-7688. by Y. H. Tan, C. Tan, J. Wang, R. Luo posted to implicit_solvation molecular_dynamics pb by onufriev on 2008-09-03 23:04:40 as along with 1 person RamuAnandakrishnan
	Insight into the role of hydration on protein dynamics. [My Copy] The Journal of chemical physics, Vol. 125, No. 9. (7 September 2006) by D. Hamelberg, T. Shen, J. A. McCammon posted to gb implicit_solvation time_scale by onufriev on 2008-08-14 07:53:52 as along with 1 person pgasper
	Potential energy functions for protein design. [My Copy] Curr Opin Struct Biol (24 March 2007) by F Edward E. Boas, Pehr B B. Harbury posted to implicit_solvation protein_folding by onufriev on 2008-08-13 02:13:24 as along with 5 people kgutwin krapnik msuarezdiez BragilMassoud aalibes
	On the Dielectric Boundary in Poisson-Boltzmann Calculations [My Copy] J. Chem. Theory Comput., Vol. 4, No. 3. (11 March 2008), pp. 507-514. by H. Tjong, H. X. Zhou posted to gb implicit_solvation pb by onufriev on 2008-08-13 02:08:57 as along with 1 person and 1 group sobolevnrm baker-group
	Recent advances in implicit solvent-based methods for biomolecular simulations. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (04 April 2008), pp. 140-148. by Jianhan Chen, Charles L. Brooks, Jana Khandogin posted to implicit_solvation molecular_dynamics by onufriev on 2008-08-13 02:04:41 as along with 8 people and 2 groups krapnik RamuAnandakrishnan mikaellund oteri nickolay flbarroso choonpeng sobolevnrm Structural Biology Group TorVergata baker-group
	Protein molecular dynamics with the generalized born/ACE solvent model [My Copy] Proteins: Structure, Function, and Genetics, Vol. 45, No. 2. (01 November 2001), pp. 144-158. by Nicolas Calimet,, Michael Schaefer,, Thomas Simonson, posted to gb implicit_solvation molecular_dynamics by onufriev on 2008-08-02 01:42:44 as along with 2 people ckmyo yxue
	Electrostatics and dynamics of proteins [My Copy] Reports of Progress in Physics, Vol. 66 (May 2003), pp. 737-787. by T. Simonson posted to electrostatics implicit_solvation molecular_dynamics by onufriev on 2008-08-02 01:38:42 as along with 3 people Lombardo_7 chiufanlee medic0747
	Effective energy function for proteins in solution [My Copy] Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 133-152. by Themis Lazaridis, Martin Karplus posted to implicit_solvation molecular_dynamics by onufriev on 2008-03-09 02:26:18 as along with 1 person edws
	Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1113-1130. by Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Kim A. Sharp posted to implicit_solvation md_dna molecular_dynamics by onufriev on 2008-03-09 01:52:28 as along with 5 people and 1 group ras Elena_Zubova sobolevnrm RamuAnandakrishnan dimka baker-group
	Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method [My Copy] Journal of Computational Chemistry, Vol. 25, No. 16. (2004), pp. 2049-2064. by Ninad V. Prabhu, Peijuan Zhu, Kim A. Sharp posted to implicit_solvation molecular_dynamics pb by onufriev on 2008-03-08 22:00:22 as along with 1 person and 1 group sobolevnrm baker-group
	Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models? [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007) by David S. Cerutti, Nathan A. Baker, Andrew J. Mccammon posted to explicit_solvation implicit_solvation by onufriev on 2008-03-08 20:55:40 as along with 2 people and 1 group flbarroso sobolevnrm baker-group
	Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. [My Copy] Journal of the American Chemical Society, Vol. 129, No. 9. (7 March 2007), pp. 2444-2445. by J. Chen, C. L. Brooks posted to implicit_solvation by onufriev on 2008-03-08 20:49:55 as along with 1 person flbarroso
	Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation [My Copy] J. Phys. Chem. B, Vol. 111, No. 7. (22 February 2007), pp. 1846-1857. by D. R. Roe, A. Okur, L. Wickstrom, V. Hornak, C. Simmerling posted to explicit_solvation gb implicit_solvation by onufriev on 2008-03-06 01:54:57 as along with 5 people and 1 group RamuAnandakrishnan flbarroso baaden choonpeng sobolevnrm baker-group
	Free energy landscape of protein folding in water: Explicit vs. implicit solvent [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (2003), pp. 148-161. by Ruhong Zhou posted to gb implicit_solvation protein_folding by onufriev on 2008-03-06 01:49:56 as along with 5 people chemrahul82 flbarroso choonpeng RamuAnandakrishnan msuarezdiez

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