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	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
	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
	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
	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 4 people 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 P. Grochowski, J. Trylska posted to implicit_solvation pb by onufriev on 2009-05-02 07:17:38 as along with 4 people and 1 group 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
	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 7 people and 2 groups 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. (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 1 person 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
	Local electrostatics algorithm for classical molecular dynamics simulations [My Copy] posted to implicit_solvation molecular_dynamics by onufriev on 2008-03-09 03:13:49 as
	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
	How Well Does Poisson-Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis [My Copy] J Phys Chem B., Vol. 110, 18680. by Tan posted to explicit_solvation implicit_solvation pb by onufriev on 2008-03-08 22:26:41 as
	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
	Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? [My Copy] Proceedings of the National Academy of Sciences, Vol. 99, No. 20. (1 October 2002), pp. 12777-12782. by Ruhong Zhou, Bruce J. Berne posted to gb implicit_solvation by onufriev on 2008-03-06 01:20:26 as along with 1 person flbarroso
	Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations [My Copy] J. Am. Chem. Soc., Vol. 125, No. 48. (3 December 2003), pp. 14841-14846. by S. Jang, E. Kim, S. Shin, Y. Pak posted to implicit_solvation protein_folding by onufriev on 2008-03-06 00:28:00 as
	Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing [My Copy] Journal of Molecular Biology, Vol. 323, No. 5. (08 November 2002), pp. 927-937. by Bojan Zagrovic, Christopher D. Snow, Michael R. Shirts, Vijay S. Pande posted to implicit_solvation protein_folding by onufriev on 2008-03-05 23:50:04 as along with 1 person georgwachter
	Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 13. (24 June 2003), pp. 7587-7592. by Jed W. Pitera, William Swope posted to implicit_solvation protein_folding by onufriev on 2008-03-05 23:45:29 as along with 1 person carlosjavierna
	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 image_charge implicit_solvation by onufriev on 2008-02-13 01:24:38 as along with 2 people dfgreen dimka
	Charge asymmetries in hydration of polar solutes. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 8. (28 February 2008), pp. 2405-2414. by D. L. Mobley, A. E. Barber, C. J. Fennell, K. A. Dill posted to water_models implicit_solvation beyond_pb by onufriev on 2008-02-08 19:36:13 as along with 4 people and 1 group flbarroso sobolevnrm dmobley middledomain baker-group
	An Assessment of Potential of Mean Force Calculations with Implicit Solvent Models [My Copy] J. Phys. Chem. B, Vol. 108, No. 42. (21 October 2004), pp. 16525-16532. by C. M. Stultz posted to implicit_solvation by onufriev on 2008-01-13 04:44:55 as
	Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 39. (25 September 2007), pp. 15230-15235. by I. Daidone, M. B. Ulmschneider, A. Di Nola, A. Amadei, J. C. Smith posted to explicit_solvation implicit_solvation molecular_dynamics by onufriev on 2007-12-28 02:03:54 as along with 3 people jjurban barmak7282 choonpeng
	Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation [My Copy] The Journal of Chemical Physics, Vol. 119, No. 9. (2003), pp. 4817-4826. by Tomasz Grycuk posted to electrostatics gb implicit_solvation by onufriev on 2007-12-09 23:21:35 as along with 1 person baaden

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implicit_solvation	60
gb	49
molecular_dynamics	36
nucleosome	36
pb	25
protein_folding	24
pka	22
electrostatics	20
dna_bending	19
histone_acetylation	19
dna	18
dna_electrostatics	15
higher_order_chromatin	15
protein_ligand	15
nucleosome_stability	13
dna_ions	12
nucleosome_assembly	11
beyond_pb	8
ions	8
water_models	8
explicit_solvation	7
gb_membrane	7
myoglobin	7
protein_dynamics	7
protein_electrostatics	7
coarse-grain	6
dielectric_in_biopolymers	6
dna_ab	6
dna_nano	5
md_dna	5
pedagogical	5
polyamines	5
surface	5
dna_stacking	4
drug_design	4
multiscale	4
ph	4
phosphorylation	4
rnai	4
image_charge	3
molecular_geometry	3
qmmm	3
rna_sec_structure	3
water_in_biopolymers	3
dna_bend	2
dna_stretching	2
ewald	2
free_energy	2
physics_philosophy	2
br	1
charge_asymmetry	1
classical_mechanics	1
coarse_grain	1
dna_md	1
extremophile	1
hnox	1
monte_carlo	1
non_equilibrium_statmech	1
nucleosome_positioning	1
nucleus	1
performance	1
physics_fundamentals	1
protein_stability	1
time_scale	1
water_molecules	1

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