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	Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices [My Copy] J. Am. Chem. Soc., Vol. 120, No. 37. (23 September 1998), pp. 9401-9409. by J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, D. A. Case posted to dna_ab by onufriev on 2008-08-08 05:53:34 as along with 2 people bmduggan Elena_Zubova
	From the Cover: Genomic characterization reveals a simple histone H4 acetylation code [My Copy] Proceedings of the National Academy of Sciences, Vol. 102, No. 15. (12 April 2005), pp. 5501-5506. by Michael F. Dion, Steven J. Altschuler, Lani F. Wu, Oliver J. Rando posted to higher_order_chromatin histone_acetylation nucleosome_assembly nucleosome_stability by onufriev on 2008-06-19 22:12:40 as
	Buried waters and internal cavities in monomeric proteins [My Copy] Protein Sci, Vol. 3, No. 8. (1 August 1994), pp. 1224-1235. by M. A. Williams, J. M. Goodfellow, J. M. Thornton posted to dielectric_in_biopolymers water_in_biopolymers by onufriev on 2008-06-15 18:16:42 as
	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
	Gaussian fluctuations and linear response in an electron transfer protein [My Copy] Proceedings of the National Academy of Sciences, Vol. 99, No. 10. (14 May 2002), pp. 6544-6549. by Thomas Simonson posted to dielectric_in_biopolymers by onufriev on 2008-01-22 22:38:15 as
	The Gaussian Generalized Born model: application to small molecules (DOI: 10.1039/b707574j) [My Copy] by Grant posted to gb molecular_geometry by onufriev on 2007-10-17 18:20:42 as
	Multiscale modeling of nucleic acids: Insights into DNA flexibility [My Copy] Biopolymers, Vol. 89, No. 9. (2008), pp. 722-731. by Yannick J. Bomble, David A. Case posted to dna_bending by onufriev on 2008-08-21 15:56:11 as along with 1 person simone
	Histone structure and nucleosome stability. [My Copy] Expert Rev Proteomics, Vol. 2, No. 5. (October 2005), pp. 719-729. by L. Mariño-Ramírez, M. G. Kann, B. A. Shoemaker, D. Landsman posted to histone_acetylation nucleosome_assembly nucleosome_stability phosphorylation by onufriev on 2008-06-19 21:37:32 as along with 2 people afenley aalibes
	Phosphorylated serine 28 of histone H3 is associated with destabilized nucleosomes in transcribed chromatin [My Copy] Nucl. Acids Res. (2 October 2007), gkm737. by Jian-Min Sun, Hou Y. Chen, Paula S. Espino, James R. Davie posted to nucleosome_stability phosphorylation by onufriev on 2008-06-19 21:10:49 as
	Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups [My Copy] Biophys. J. (4 January 2008), biophysj.107.122473. by Jamie L. Schlessman, Colby Abe, Apostolos Gittis, Daniel A. Karp, Michael A. Dolan, Bertrand Garcia-Moreno posted to dielectric_in_biopolymers water_in_biopolymers by onufriev on 2008-06-15 18:49:53 as along with 2 people and 1 group paulschlesinger sobolevnrm baker-group
	Effect of Phosphorylation on α-Helix Stability as a Function of Position [My Copy] Biochemistry, Vol. 41, No. 6. (12 February 2002), pp. 1897-1905. by C. D. Andrew, J. Warwicker, G. R. Jones, A. J. Doig posted to nucleosome phosphorylation by onufriev on 2008-04-16 20:29:14 as
	Variability in the pKa of histidine side-chains correlates with burial within proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 49, No. 1. (2002), pp. 1-6. by Stephen P. Edgcomb, Kenneth P. Murphy posted to pka by onufriev on 2008-02-12 22:31:33 as
	Solvent mobility and the protein 'glass' transition. [My Copy] Nat Struct Biol, Vol. 7, No. 1. (January 2000), pp. 34-38. by D. Vitkup, D. Ringe, G. A. Petsko, M. Karplus posted to myoglobin protein_dynamics by onufriev on 2008-01-25 02:22:48 as along with 4 people abovell saravan naitsabes jteyra
	Polar fluctuations in proteins: molecular-dynamic studies of cytochrome c in aqueous solution. [My Copy] Faraday Discuss, No. 103. (1996), pp. 71-90. by T. Simonson, D. Perahia posted to dielectric_in_biopolymers by onufriev on 2008-01-22 22:40:21 as
	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
	Nucleosome stability mediated by histone variants H3.3 and H2A.Z [My Copy] Genes Dev., Vol. 21, No. 12. (15 June 2007), pp. 1519-1529. by Chunyuan Jin, Gary Felsenfeld posted to nucleosome nucleosome_stability by onufriev on 2007-12-11 22:00:08 as along with 1 person sebastien_vigneau
	An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution [My Copy] Journal of Molecular Biology, Vol. 256, No. 5. (15 March 1996), pp. 939-948. by F. Fraternali, W. F. van Gunsteren posted to molecular_dynamics implicit_solvation by onufriev on 2007-12-06 19:52:23 as
	Sir2 Deacetylates Histone H3 Lysine 56 to Regulate Telomeric Heterochromatin Structure in Yeast [My Copy] Molecular Cell, Vol. 27, No. 6. (21 September 2007), pp. 890-900. by Feng Xu, Qiongyi Zhang, Kangling Zhang, Wei Xie, Michael Grunstein posted to histone_acetylation nucleosome by onufriev on 2007-11-29 22:50:19 as along with 2 people gderwin zhlei
	Specific Contributions of Histone Tails and their Acetylation to the Mechanical Stability of Nucleosomes [My Copy] Journal of Molecular Biology, Vol. 346, No. 1. (11 February 2005), pp. 135-146. by Brent Brower-Toland, David A. Wacker, Robert M. Fulbright, John T. Lis, Lee W. Kraus, Michelle D. Wang posted to nucleosome nucleosome_assembly by onufriev on 2007-11-11 04:07:57 as
	Split Decision: What Happens to Nucleosomes during DNA Replication? [My Copy] J. Biol. Chem., Vol. 280, No. 13. (1 April 2005), pp. 12065-12068. by Anthony T. Annunziato posted to nucleosome nucleosome_assembly by onufriev on 2007-11-10 20:48:35 as
	Polyamine-dependent gene expression. [My Copy] Cell Mol Life Sci, Vol. 60, No. 7. (July 2003), pp. 1394-1406. by A. C. Childs, D. J. Mehta, E. W. Gerner posted to higher_order_chromatin nucleosome polyamines by onufriev on 2007-11-09 06:11:16 as
	High concentration of DNA in condensed chromatin [My Copy] by Daban J-R posted to higher_order_chromatin nucleosome by onufriev on 2007-11-08 23:20:46 as
	Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 1100-1105. by Bernd Ensing, Steven O. Nielsen, Preston B. Moore, Michael L. Klein, Michele Parrinello posted to molecular_dynamics by onufriev on 2007-11-08 00:05:51 as along with 1 person RamuAnandakrishnan
	An electrostatic model of B-DNA for its stability against unwinding [My Copy] Biophysical Chemistry, Vol. 75, No. 3. (14 December 1998), pp. 229-233. by Dirk Stigter posted to dna_electrostatics by onufriev on 2007-11-04 16:06:04 as
	Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm [My Copy] Journal of Computational Chemistry, Vol. 24, No. 16. (2003), pp. 2063-2074. by Qing Zhang, Daniel A. Beard, Tamar Schlick posted to dna_electrostatics electrostatics implicit_solvation by onufriev on 2007-10-31 22:02:58 as
	From the Cover: Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA [My Copy] Proceedings of the National Academy of Sciences, Vol. 99, No. 4. (19 February 2002), pp. 1960-1965. by Brent D. Brower-Toland, Corey L. Smith, Richard C. Yeh, John T. Lis, Craig L. Peterson, Michelle D. Wang posted to nucleosome by onufriev on 2007-10-30 01:48:03 as along with 1 person afenley
	Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation [My Copy] The Journal of Physical Chemistry B, Vol. 104, No. 15. (1 April 2000), pp. 3668-3675. by Wolfgang Weber, Philippe H. Hunenberger, J. Andrew Mccammon posted to ewald protein_electrostatics by onufriev on 2007-10-22 22:46:06 as along with 1 person r2s2
	A generalized reaction field method for molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 102, No. 13. (1995), pp. 5451-5459. by Ilario G. Tironi, René Sperb, Paul E. Smith, Wilfred F. van Gunsteren posted to molecular_dynamics implicit_solvation by onufriev on 2007-10-02 00:14:08 as along with 3 people r2s2 dsmueller RamuAnandakrishnan
	Inclusion of ionization states of ligands in affinity calculations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 1. (2009), pp. 138-150. by Serena Donnini, Alessandra Villa, Gerrit Groenhof, Alan E. Mark, Rik K. Wierenga, André H. Juffer posted to protein_ligand pka by onufriev on 2009-11-04 23:52:27 as along with 4 people and 2 groups rbaron ibuch sobolevnrm RamuAnandakrishnan McCammon baker-group
	Generalized Formula for the Electric Tunnel Effect between Similar Electrodes Separated by a Thin Insulating Film [My Copy] Journal of Applied Physics, Vol. 34, No. 6. (1963), pp. 1793-1803. by John G. Simmons posted to image_charge electrostatics by onufriev on 2009-11-04 23:43:24 as along with 2 people mountain4bike taro
	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
	Electric fields at the active site of an enzyme: direct comparison of experiment with theory. [My Copy] Science (New York, N.Y.), Vol. 313, No. 5784. (14 July 2006), pp. 200-204. by Ian T. Suydam, Christopher D. Snow, Vijay S. Pande, Steven G. Boxer posted to pb electrostatics by onufriev on 2009-10-29 06:13:17 as along with 5 people charris5 flbarroso mikaellund jbchang kjell
	Life in extreme environments [My Copy] Nature, Vol. 409, No. 6823. (22 February 2001), pp. 1092-1101. by Lynn J. Rothschild, Rocco L. Mancinelli posted to extremophile by onufriev on 2009-10-13 19:55:59 as along with 2 people qshao afon
	The relation between momentum conservation and Newton's third law revisited [My Copy] (16 Jan 2006) by Rodolfo A. Diaz, William J. Herrera posted to physics_fundamentals classical_mechanics by onufriev on 2009-10-11 18:44:43 as
	Coherent emission of light by thermal sources [My Copy] Nature, Vol. 416, No. 6876. (07 March 2002), pp. 61-64. by Jean-Jacques Greffet, Remi Carminati, Karl Joulain, Jean-Philippe Mulet, Stephane Mainguy, Yong Chen posted to physics_philosophy by onufriev on 2009-10-11 18:29:35 as along with 1 person Elena_Zubova
	Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes [My Copy] Journal of the American Chemical Society, Vol. 126, No. 9. (1 March 2004), pp. 2862-2869. by P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, J. Chattopadhyaya posted to pka dna by onufriev on 2009-10-11 03:09:39 as
	More Is Different [My Copy] Science (0 1972) by P. W. Anderson posted to physics_philosophy by onufriev on 2009-10-07 01:03:37 as
	On the pH dependence of protein stability. [My Copy] Journal of molecular biology, Vol. 231, No. 2. (20 May 1993), pp. 459-474. by A. S. Yang, B. Honig posted to protein_stability pka ph by onufriev on 2009-09-24 14:31:24 as along with 3 people and 1 group scampos flbarroso cat_worth structural_bioinformatics
	Computational alanine scanning of protein-protein interfaces. [My Copy] Science's STKE : signal transduction knowledge environment, Vol. 2004, No. 219. (10 February 2004) by Tanja Kortemme, David E. Kim, David Baker posted to protein_ligand pka by onufriev on 2009-08-26 02:25:09 as along with 7 people and 6 groups pablocarb bicko barry sangeetha blackbart joergkurtwegner skoddet structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	A simple physical model for binding energy hot spots in protein-protein complexes. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121. by Tanja Kortemme, David Baker posted to protein_ligand by onufriev on 2009-08-26 02:22:57 as along with 7 people and 1 group oceanwind lna jwm bicko cjeans hmk skoddet Nielsen group
	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
	On removal of charge singularity in Poisson--Boltzmann equation [My Copy] The Journal of Chemical Physics, Vol. 130, No. 14. (2009), 145101. by Qin Cai, Jun Wang, Hong K. Zhao, Ray Luo posted to pb by onufriev on 2009-08-14 02:47:18 as along with 1 person and 1 group sobolevnrm 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
	Counterion condensation and fluctuation-induced attraction [My Copy] Physical Review E, Vol. 66, No. 4. (Oct 2002), 041501. by A. W. C. Lau, P. Pincus posted to ions by onufriev on 2009-08-13 23:24:36 as
	Giant charge inversion of a macroion due to multivalent counterions and monovalent coions: Molecular dynamics study [My Copy] The Journal of Chemical Physics, Vol. 115, No. 1. (2001), pp. 567-574. by Motohiko Tanaka, A. Yu Grosberg posted to ions dna_ions by onufriev on 2009-08-13 23:19:20 as
	Where the linearized Poisson--Boltzmann cell model fails: Spurious phase separation in charged colloidal suspensions [My Copy] The Journal of Chemical Physics, Vol. 119, No. 3. (2003), pp. 1855-1865. by M. N. Tamashiro, H. Schiessel posted to pb by onufriev on 2009-08-13 23:17:37 as along with 1 person softsimu
	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
	Attraction between DNA molecules mediated by multivalent ions [My Copy] Physical Review E, Vol. 69, No. 4. (Apr 2004), 041904. by E. Allahyarov, G. Gompper, H. Löwen posted to dna_ions dna_electrostatics dna by onufriev on 2009-08-13 23:12:18 as

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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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