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sobolevnrm nucleic_acids [417 articles]

Recent papers added to sobolevnrm library classified by the tag nucleic_acids. You can also see everyone's nucleic_acids.
  • Liquid Crystalline Phase Behavior of High Molecular Weight DNA: A Comparative Study of the Influence of Metal Ions of Different Size, Charge and Binding Mode
    Biomacromolecules, Vol. 9, No. 7. (2008), pp. 1860-1869.
    by Neethu Sundaresan, Cherumuttathu H Suresh, Thresia Thomas, TJ Thomas, CKS Pillai
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-08-01 12:50:48 as read
  • Liquid Crystalline Phase Behavior of High Molecular Weight DNA: A Comparative Study of the Influence of Metal Ions of Different Size, Charge and Binding Mode
    Biomacromolecules, Vol. 9, No. 7. (14 July 2008), pp. 1860-1869.
    by Neethu Sundaresan, Cherumuttathu H Suresh, Thresia Thomas, TJ Thomas, CKS Pillai
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-07-25 12:02:47 as read along with 1 group baker-group
  • Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane
    Biophys. J., Vol. 82, No. 1. (1 January 2002), pp. 76-92.
    by Christian Fleck, Roland R Netz, Hans H von Grunberg
    posted to biomembranes electrostatics nucleic_acids pka solvation by sobolevnrm on 2008-07-16 16:02:20 as read along with 2 people and 1 group softsimu rok baker-group
  • Assessing the performance of implicit solvation models at a nucleic acid surface
    Physical Chemistry Chemical Physics (in press)
    by F Dong, JA Wagoner, NA Baker
    posted to electrostatics nonpolar nucleic_acids solvation by sobolevnrm on 2008-07-08 12:27:15 as read along with 1 group baker-group
  • Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the Stability of RNA Hairpins
    J. Am. Chem. Soc., Vol. 130, No. 23. (11 June 2008), pp. 7364-7372.
    by David L Pincus, Changbong Hyeon, D Thirumalai
    posted to nucleic_acids solvation by sobolevnrm on 2008-07-08 11:59:21 as read along with 1 group baker-group
  • Solvation Free Energies of the Nucleic Acid Bases
    J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8587-8594.
    by JL Miller, PA Kollman
    posted to molecular_simulation nucleic_acids solvation by sobolevnrm on 2008-06-30 12:15:23 as read along with 1 group baker-group
  • Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory
    The Journal of Chemical Physics, Vol. 128, No. 18. (2008)
    by Yoshiteru Yonetani, Yutaka Maruyama, Fumio Hirata, Hidetoshi Kono
    posted to electrostatics integral_equation nucleic_acids solvation by sobolevnrm on 2008-06-27 12:08:04 as read along with 1 group baker-group
  • Mono- and Trivalent Ions around DNA: A Small-Angle Scattering Study of Competition and Interactions
    Biophys. J., Vol. 95, No. 1. (1 July 2008), pp. 287-295.
    by Kurt Andresen, Xiangyun Qiu, Suzette A Pabit, Jessica S Lamb, Hye Y Park, Lisa W Kwok, Lois Pollack
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-06-16 18:15:25 as read along with 1 group baker-group
  • The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
    Journal of Computational Chemistry (in press)
    by M Gruziel, P Grochowski, J Trylska
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-05-27 11:34:49 as read along with 1 group baker-group
  • Solvent Structure and Hammerhead Ribozyme Catalysis
    Chemistry & Biology, Vol. 15, No. 4. (21 April 2008), pp. 332-342.
    by Monika Martick, Tai-Sung Lee, Darrin M York, William G Scott
    posted to nucleic_acids solvation by sobolevnrm on 2008-05-27 11:19:49 as read along with 1 group baker-group
  • Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations
    Biochemistry, Vol. 47, No. 19. (13 May 2008), pp. 5336-5353.
    by Richard Owczarzy, Bernardo G Moreira, Yong You, Mark A Behlke, Joseph A Walder
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-05-22 12:05:00 as read along with 1 group baker-group
  • Targeted Quantum Dot Conjugates for siRNA Delivery.
    Bioconjug Chem (14 July 2007)
    by Austin M Derfus, Alice A Chen, Dal-Hee H Min, Erkki Ruoslahti, Sangeeta N Bhatia
    posted to cancer ccne nanotech nucleic_acids drugdesign by sobolevnrm on 2008-05-15 11:51:36 as ** along with 2 people and 1 group jyuh ml115 baker-group
  • Quantum dots to monitor RNAi delivery and improve gene silencing
    Nucleic Acids Research, Vol. 33, No. 22. (2005), pp. e190-e190.
    by Alice A Chen, Austin M Derfus, Salman R Khetani, Sangeeta N Bhatia
    posted to ccne imaging nanotech nucleic_acids drugdesign by sobolevnrm on 2008-05-15 11:46:38 as read along with 1 person and 1 group ml115 baker-group
  • Association of Aminoglycosidic Antibiotics with the Ribosomal A-Site Studied with Brownian Dynamics
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 549-559.
    by Maciej Długosz, Jan M Antosiewicz, Joanna Trylska
    posted to diffusion electrostatics nucleic_acids by sobolevnrm on 2008-05-12 12:08:13 as read along with 1 person and 2 groups barry baker-group McCammon
  • Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method
    Chemical Physics Letters, Vol. 454, No. 4-6. (20 March 2008), pp. 391-395.
    by Donghong Min, Hongzhi Li, Guohui Li, Bernd A Berg, Marcia O Fenley, Wei Yang
    posted to electrostatics molecular_simulation nucleic_acids statistical_mechanics by sobolevnrm on 2008-05-08 11:41:20 as read along with 1 group baker-group
  • Enhanced delivery of antisense oligonucleotides with fluorophore-conjugated PAMAM dendrimers
    Nucl. Acids Res., Vol. 28, No. 21. (1 November 2000), pp. 4225-4231.
    by Hoon Yoo, RL Juliano
    posted to ccne imaging nanotech nucleic_acids by sobolevnrm on 2008-05-08 11:18:40 as read along with 1 person and 1 group ml115 baker-group
  • Intracellular delivery of an anionic antisense oligonucleotide via receptor-mediated endocytosis
    Nucl. Acids Res. (26 March 2008), gkn115.
    by Md R Alam, Vidula Dixit, Hyunmin Kang, Zi-Bo Li, Xiaoyaun Chen, Joann Trejo, Michael Fisher, Rudy L Juliano
    posted to ccne nanotech nucleic_acids by sobolevnrm on 2008-05-08 11:18:10 as read along with 1 person and 1 group ml115 baker-group
  • PAMAM Dendrimers as Delivery Agents for Antisense Oligonucleotides
    Pharmaceutical Research, Vol. 16, No. 12. (1 December 1999), pp. 1799-1804.
    by Hoon Yoo, Peter Sazani, RL Juliano
    posted to ccne nanotech nucleic_acids by sobolevnrm on 2008-05-08 11:17:42 as read along with 1 group baker-group
  • Characterization of complexes of oligonucleotides with polyamidoamine starburst dendrimers and effects on intracellular delivery
    Journal of Pharmaceutical Sciences, Vol. 86, No. 6. (1997), pp. 762-764.
    by Robert Delong, Katherine Stephenson, Todd Loftus, Michael Fisher, Suresh Alahari, Arno Nolting, RL Juliano
    posted to ccne nanotech nucleic_acids by sobolevnrm on 2008-05-07 11:35:40 as read along with 1 person and 1 group ml115 baker-group
  • Low-Frequency Electrophoretic Actuation of Nanoscale Optoentropic Transduction Mechanisms
    Nano Lett., Vol. 7, No. 4. (11 April 2007), pp. 950-955.
    by BD Sullivan, DA Dehlinger, S Zlatanovic, SA Esener, MJ Heller
    posted to ccne imaging nanotech nucleic_acids by sobolevnrm on 2008-05-07 11:19:53 as read along with 1 person and 1 group ml115 baker-group
  • Oligonucleotide-Modified Gold Nanoparticles for Intracellular Gene Regulation
    Science, Vol. 312, No. 5776. (19 May 2006), pp. 1027-1030.
    by Nathaniel L Rosi, David A Giljohann, Shad C Thaxton, Abigail K Lytton-Jean, Min S Han, Chad A Mirkin
    posted to ccne nanotech nucleic_acids by sobolevnrm on 2008-05-07 11:18:57 as read along with 1 person and 1 group ml115 baker-group
  • Screening the Sequence Selectivity of DNA-Binding Molecules Using a Gold Nanoparticle-Based Colorimetric Approach
    Anal. Chem., Vol. 79, No. 18. (15 September 2007), pp. 7201-7205.
    by SJ Hurst, MS Han, AKR Lytton-Jean, CA Mirkin
    posted to ccne nanotech nucleic_acids by sobolevnrm on 2008-05-07 11:18:12 as read along with 1 person and 1 group ml115 baker-group
  • Maximizing DNA Loading on a Range of Gold Nanoparticle Sizes
    Anal. Chem., Vol. 78, No. 24. (15 December 2006), pp. 8313-8318.
    by SJ Hurst, AKR Lytton-Jean, CA Mirkin
    posted to ccne nanotech nucleic_acids by sobolevnrm on 2008-05-07 11:17:49 as read along with 1 person and 1 group ml115 baker-group
  • Electrostatic Free Energy Landscapes for DNA Helix Bending
    Biophys. J., Vol. 94, No. 8. (15 April 2008), pp. 3137-3149.
    by Zhi-Jie Tan, Shi-Jie Chen
    posted to electrostatics nucleic_acids statistical_mechanics by sobolevnrm on 2008-05-05 11:11:06 as read along with 2 people and 1 group sunhwan Elena_Zubova baker-group
  • Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules
    Physical Review Letters, Vol. 100, No. 11. (2008)
    by Liang Dai, Yuguang Mu, Lars Nordenskiöld, Johan RC van der Maarel
    posted to electrostatics nucleic_acids by sobolevnrm on 2008-05-02 11:13:36 as read along with 1 person and 1 group kkims baker-group
  • DNA and its counterions: a molecular dynamics study.
    Nucleic Acids Res, Vol. 32, No. 14. (2004), pp. 4269-4280.
    by P Várnai, K Zakrzewska
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-29 19:40:21 as read along with 1 group baker-group
  • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    Biopolymers, Vol. 56, No. 4. (2001), pp. 232-256.
    by Iii Cheatham, MA Young
    posted to electrostatics molecular_dynamics nucleic_acids solvation by sobolevnrm on 2008-04-29 19:38:40 as read along with 1 group baker-group
  • Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
    Nucl. Acids Res. (14 February 2008), gkn008.
    by Yao C Chen, Carmay Lim
    posted to bioinformatics electrostatics nucleic_acids protein-nucleic_acid_interactions structure by sobolevnrm on 2008-04-29 11:22:50 as read along with 3 people and 1 group kaarsinogen sunhwan marck baker-group
  • Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E
    Biophys. J., Vol. 84, No. 6. (1 June 2003), pp. 3564-3582.
    by Kamila Reblova, Nad'a Spackova, Richard Stefl, Kristina Csaszar, Jaroslav Koca, Neocles B Leontis, Jiri Sponer
    posted to nucleic_acids solvation by sobolevnrm on 2008-04-25 16:19:17 as read along with 1 group baker-group
  • Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability
    Proceedings of the National Academy of Sciences, Vol. 104, No. 30. (24 July 2007), pp. 12336-12340.
    by Michael T Sykes, Michael Levitt
    posted to nucleic_acids solvation by sobolevnrm on 2008-04-25 16:16:00 as read along with 1 group baker-group
  • Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding
    Journal of Molecular Biology, Vol. 313, No. 5. (9 November 2001), pp. 1073-1091.
    by Kristina Csaszar, Nad'a Spacková, Richard Stefl, Jirí Sponer, Neocles B Leontis
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 15:54:39 as read along with 1 group baker-group
  • Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator
    Journal of Molecular Biology, Vol. 282, No. 4. (2 October 1998), pp. 859-873.
    by Alexandre M Bonvin, Maria Sunnerhagen, Gottfried Otting, Wilfred F van Gunsteren
    posted to electrostatics nucleic_acids protein-nucleic_acid_interactions solvation by sobolevnrm on 2008-04-25 15:52:31 as read along with 1 group baker-group
  • RNA solvation: A molecular dynamics simulation perspective
    Biopolymers, Vol. 56, No. 4. (2000), pp. 266-274.
    by Pascal Auffinger, Eric Westhof
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 15:43:05 as read along with 1 group baker-group
  • A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.
    Biophys. J., Vol. 73, No. 5. (1 November 1997), pp. 2313-2336.
    by MA Young, G Ravishanker, DL Beveridge
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 15:37:20 as read along with 1 group baker-group
  • NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex
    Journal of Molecular Biology, Vol. 302, No. 5. (6 October 2000), pp. 1101-1117.
    by Vickie Tsui, Ishwar Radhakrishnan, Peter E Wright, David A Case
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 15:30:08 as read along with 1 group baker-group
  • Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.
    J Mol Biol, Vol. 305, No. 5. (2 February 2001), pp. 1057-1072.
    by P Auffinger, E Westhof
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 15:07:46 as read along with 1 person and 1 group lillekatt baker-group
  • Water and ion binding around RNA and DNA (C,G) oligomers.
    J Mol Biol, Vol. 300, No. 5. (28 July 2000), pp. 1113-1131.
    by P Auffinger, E Westhof
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 15:04:29 as read along with 2 people and 1 group lillekatt ffranca baker-group
  • Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation
    Journal of Molecular Biology, Vol. 286, No. 4. (5 March 1999), pp. 1075-1095.
    by Michael Feig, Montgomery B Pettitt
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 15:00:38 as read along with 1 group baker-group
  • A molecular simulation picture of DNA hydration around A- and B-DNA
    Biopolymers, Vol. 48, No. 4. (1998), pp. 199-209.
    by Michael Feig, Montgomery B Pettitt
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-04-25 14:56:37 as read along with 1 group baker-group
  • Recent advances in the study of nucleic acid flexibility by molecular dynamics
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Modesto Orozco, Agnes Noy, Alberto Pérez
    posted to molecular_simulation nucleic_acids by sobolevnrm on 2008-04-15 11:50:15 as read along with 2 people and 1 group onufriev mazo baker-group
  • Dynamics of Recognition between tRNA and Elongation Factor Tu
    Journal of Molecular Biology, Vol. 377, No. 5. (11 April 2008), pp. 1382-1405.
    by John Eargle, Alexis A Black, Anurag Sethi, Leonardo G Trabuco, Zaida Luthey-Schulten
    posted to allostery electrostatics nucleic_acids protein-nucleic_acid_interactions by sobolevnrm on 2008-03-25 11:14:57 as read along with 1 group baker-group
  • Nanoparticulate delivery of suicide DNA to murine prostate and prostate tumors
    The Prostate, Vol. 67, No. 8. (2007), pp. 855-862.
    by Weidan Peng, Daniel G Anderson, Yunhua Bao, Robert F Padera, Robert Langer, Janet A Sawicki
    posted to cancer ccne nanotech nucleic_acids drugdesign by sobolevnrm on 2008-03-12 11:22:23 as read along with 1 person and 1 group ml115 baker-group
  • Interplay of ion binding and attraction in DNA condensed by multivalent cations
    Nucl. Acids Res., Vol. 36, No. 2. (2 February 2008), pp. 501-510.
    by Brian A Todd, Donald C Rau
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-02-29 12:40:03 as read along with 1 person and 2 groups skoch3 baker-group Koch_Lab
  • Structure and Dynamics of Poly(T) Single-Strand DNA: Implications toward CPD Formation
    J. Phys. Chem. B, Vol. 111, No. 51. (27 December 2007), pp. 14398-14404.
    by AT Johnson, O Wiest
    posted to molecular_dynamics molecular_simulation nucleic_acids by sobolevnrm on 2008-02-01 12:50:34 as read along with 1 group baker-group
  • Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin
    J. Am. Chem. Soc., Vol. 130, No. 3. (23 January 2008), pp. 815-817.
    by AE Garcia, D Paschek
    posted to molecular_dynamics molecular_simulation nucleic_acids by sobolevnrm on 2008-01-30 12:42:58 as read along with 1 group baker-group
  • Visualizing spatially correlated dynamics that directs RNA conformational transitions
    Nature, Vol. 450, No. 7173., pp. 1263-1267.
    by Qi Zhang, Andrew C Stelzer, Charles K Fisher, Hashim M Al-Hashimi
    posted to molecular_dynamics nmr nucleic_acids by sobolevnrm on 2008-01-29 12:25:38 as read along with 7 people and 3 groups cactus niallhaslam joseph_x_zhou kintoki kluck nigham simone baker-group HIV_DR Soft Matter
  • Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ninad V Prabhu, Manoranjan Panda, Qingyi Yang, Kim A Sharp
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-01-21 12:55:09 as read along with 3 people and 1 group RamuAnandakrishnan onufriev dimka baker-group
  • Interplay of ion binding and attraction in DNA condensed by multivalent cations
    Nucleic Acids Research (in press)
    by BA Todd, DC Rau
    posted to electrostatics nucleic_acids by sobolevnrm on 2008-01-03 12:21:47 as read along with 1 group baker-group
  • Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin
    Nucl. Acids Res., Vol. 35, No. 20. (29 November 2007), pp. 6995-7002.
    by Zhuoyun Zhuang, Luc Jaeger, Joan-Emma Shea
    posted to molecular_simulation nucleic_acids protein_folding by sobolevnrm on 2008-01-02 12:32:22 as read along with 1 group baker-group
  • Dynamics of B-DNA on the Microsecond Time Scale
    J. Am. Chem. Soc., Vol. 129, No. 47. (28 November 2007), pp. 14739-14745.
    by A Perez, FJ Luque, M Orozco
    posted to electrostatics molecular_simulation nucleic_acids solvation by sobolevnrm on 2007-12-17 13:00:05 as read along with 1 person and 1 group Elena_Zubova baker-group
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