onufriev's library 300 articles Export

	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
	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
	Symmetry breaking and electrostatic attraction between two identical surfaces [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 4. (2009), 041404. by F. Plouraboué, H. C. Chang posted to pb ions dna_ions by onufriev on 2009-08-13 23:05:42 as along with 2 people and 1 group jeevanjyoti sobolevnrm baker-group
	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
	Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships [My Copy] J. Virol., Vol. 83, No. 13. (1 July 2009), pp. 6326-6334. by Susan J. Schroeder posted to rna_sec_structure rnai by onufriev on 2009-08-02 20:51:36 as along with 3 people samgj kieran101 carlosjavierna
	Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies [My Copy] Journal of the American Chemical Society, Vol. 121, No. 36. (1 September 1999), pp. 8133-8143. by Irina Massova, Peter A. Kollman posted to protein_ligand by onufriev on 2009-07-18 07:58:40 as along with 1 person boris_aguilar
	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
	Protein folding by zipping and assembly. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 29. (17 July 2007), pp. 11987-11992. by S. B. Ozkan, G. A. Wu, J. D. Chodera, K. A. Dill posted to gb protein_folding by onufriev on 2009-06-21 05:39:45 as along with 4 people aqeel wouterboomsma cdeane ARobson
	Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification [My Copy] J. Biol. Chem. (21 December 2006), M607909200. by Stephanie A. Morris, Bhargavi Rao, Benjamin A. Garcia, et al.Sandra B. Hake, Robert L. Diaz, Jeffrey Shabanowitz, Donald F. Hunt, David C. Allis, Jason D. Lieb, Brian D. Strahl posted to histone_acetylation nucleosome by onufriev on 2009-06-17 06:53:14 as
	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
	30 nm Chromatin Fibre Decompaction Requires both H4-K16 Acetylation and Linker Histone Eviction [My Copy] Journal of Molecular Biology, Vol. 381, No. 4. (12 September 2008), pp. 816-825. by Philip J. Robinson, Woojin An, Andrew Routh, et al.Fabrizio Martino, Lynda Chapman, Robert G. Roeder, Daniela Rhodes posted to higher_order_chromatin by onufriev on 2009-06-15 22:33:42 as
	Proliferating cell nuclear antigen and ASF1 modulate silent chromatin in Saccharomyces cerevisiae via lysine 56 on histone H3. [My Copy] Genetics, Vol. 179, No. 2. (June 2008), pp. 793-809. by A. Miller, B. Yang, T. Foster, A. L. Kirchmaier posted to no-tag by onufriev on 2009-06-15 07:22:52 as along with 2 people gderwin Petersarkies
	Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles [My Copy] Nucl. Acids Res., Vol. 37, No. 9. (1 May 2009), pp. 2882-2893. by Davide Demurtas, Arnaud Amzallag, Eric J. Rawdon, John H. Maddocks, Jacques Dubochet, Andrzej Stasiak posted to dna dna_bending by onufriev on 2009-06-14 07:37:48 as
	Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. [My Copy] Cell, Vol. 127, No. 7. (29 December 2006), pp. 1361-1373. by M. V. Botuyan, J. Lee, I. M. Ward, et al.J. E. Kim, J. R. Thompson, J. Chen, G. Mer posted to histone_acetylation nucleosome by onufriev on 2009-06-14 01:04:59 as along with 1 person DNAReplication
	Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions [My Copy] Nature, Vol. 458, No. 7238. (2 April 2009), pp. 591-596. by Peter J. Cook, Bong G. Ju, Francesca Telese, Xiangting Wang, Christopher K. Glass, Michael G. Rosenfeld posted to nucleosome by onufriev on 2009-06-12 00:39:00 as along with 4 people wmatsui fenghezi DevilInPgh paulschlesinger
	Histone H4 lysine 91 acetylation a core domain modification associated with chromatin assembly. [My Copy] Molecular cell, Vol. 18, No. 1. (1 April 2005), pp. 123-130. by J. Ye, X. Ai, E. E. Eugeni, et al.L. Zhang, L. R. Carpenter, M. A. Jelinek, M. A. Freitas, M. R. Parthun posted to histone_acetylation nucleosome nucleosome_assembly by onufriev on 2009-05-31 00:06:24 as
	Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. [My Copy] Science (New York, N.Y.), Vol. 315, No. 5812. (2 February 2007), pp. 649-652. by R. Driscoll, A. Hudson, S. P. Jackson posted to histone_acetylation nucleosome by onufriev on 2009-05-30 00:36:01 as
	Acetylated Lysine 56 on Histone H3 Drives Chromatin Assembly after Repair and Signals for the Completion of Repair [My Copy] Cell, Vol. 134, No. 2. (25 July 2008), pp. 231-243. by Chin-Chuan Chen, Joshua J. Carson, Jason Feser, et al.Beth Tamburini, Susan Zabaronick, Jeffrey Linger, Jessica K. Tyler posted to higher_order_chromatin histone_acetylation nucleosome nucleosome_assembly by onufriev on 2009-05-30 00:32:42 as along with 2 people vega inesdesantiago
	Histone H3 K56 acetylation, chromatin assembly, and the DNA damage checkpoint [My Copy] DNA Repair, Vol. 7, No. 12. (01 December 2008), pp. 2020-2024. by J. Downs posted to histone_acetylation nucleosome by onufriev on 2009-05-29 04:08:21 as along with 1 person gderwin
	A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response [My Copy] Nature, Vol. 436, No. 7048., pp. 294-298. by Hiroshi Masumoto, David Hawke, Ryuji Kobayashi, Alain Verreault posted to histone_acetylation nucleosome by onufriev on 2009-05-29 04:04:12 as along with 1 person gderwin
	Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry. [My Copy] Analytical biochemistry, Vol. 306, No. 2. (15 July 2002), pp. 259-269. by K. Zhang, H. Tang, L. Huang, et al.J. W. Blankenship, P. R. Jones, F. Xiang, P. M. Yau, A. L. Burlingame posted to histone_acetylation nucleosome by onufriev on 2009-05-27 06:23:58 as
	Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. [My Copy] Genes & development, Vol. 16, No. 12. (15 June 2002), pp. 1518-1527. by H. H. Ng, Q. Feng, H. Wang, et al.H. Erdjument-Bromage, P. Tempst, Y. Zhang, K. Struhl posted to nucleosome by onufriev on 2009-05-27 06:21:25 as
	Chromatin Fiber Folding: Requirement for the Histone H4 N-terminal Tail [My Copy] Journal of Molecular Biology, Vol. 327, No. 1. (14 March 2003), pp. 85-96. by B. Dorigo posted to higher_order_chromatin histone_acetylation nucleosome by onufriev on 2009-05-27 05:59:02 as
	How does the histone code work? [My Copy] Biochemistry and cell biology = Biochimie et biologie cellulaire, Vol. 83, No. 4. (August 2005), pp. 468-476. by M. S. Cosgrove, C. Wolberger posted to histone_acetylation nucleosome nucleosome_stability by onufriev on 2009-05-23 07:11:25 as
	Regulated nucleosome mobility and the histone code [My Copy] Nature Structural & Molecular Biology, Vol. 11, No. 11. (02 November 2004), 1037. by Michael S. Cosgrove, Jef D. Boeke, Cynthia Wolberger posted to nucleosome nucleosome_stability by onufriev on 2009-05-23 07:06:58 as along with 1 person afenley
	Nucleosome destabilization in the epigenetic regulation of gene expression [My Copy] Nat Rev Genet, Vol. 9, No. 1. (4 January 2008), pp. 15-26. by Steven Henikoff posted to histone_acetylation nucleosome nucleosome_stability by onufriev on 2009-05-23 06:55:56 as along with 4 people inesdesantiago tonamswish Petersarkies dchughes

Note: You may cite this page as: http://www.citeulike.org/user/onufriev

Result page: 1 2 3 4 5 6 Next

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

onufriev's library 300 articles Export

onufriev's tags