Group: baker-group - with tag protein-nucleic_acid_interactions [104 articles] Export

Recent papers posted by members of the baker-group group with tag protein-nucleic_acid_interactions

	Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 18. (5 May 2009), pp. 7449-7454. by Hanbin Liu, Yemin Shi, Xiaojiang S. Chen, Arieh Warshel posted to diffusion electrostatics protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2009-05-07 12:59:56 as along with 1 person and 1 group barry McCammon
	Bulk-mediated surface diffusion along a cylinder: Propagators and crossovers [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 4. (2009), 040105. by Aleksei V. Chechkin, Irwin M. Zaid, Michael A. Lomholt, Igor M. Sokolov, Ralf Metzler posted to diffusion protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2009-04-28 12:22:33 as
	Dynamical networks in tRNA:protein complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6620-6625. by Anurag Sethi, John Eargle, Alexis A. Black, Zaida Luthey-Schulten posted to allostery graph_theory nucleic_acids protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2009-04-23 12:31:29 as along with 4 people and 1 group anuragsethi jeargle AbnerCYH jmccammon McCammon
	Efficient optimization of electrostatic interactions between biomolecules [My Copy] Decision and Control, 2007 46th IEEE Conference on In Decision and Control, 2007 46th IEEE Conference on (2007), pp. 4563-4569. by J. P. Bardhan, M. D. Altman, J. K. White, B. Tidor posted to electrostatics optimization protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2009-04-21 12:31:06 as
	Nuance in the double-helix and its role in protein–DNA recognition [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 2. (April 2009), pp. 171-177. by Remo Rohs, Sean M. West, Peng Liu, Barry Honig posted to protein-nucleic_acid_interactions review by sobolevnrm to the group baker-group on 2009-04-21 12:29:27 as
	Identification of DNA-binding proteins using structural, electrostatic and evolutionary features [My Copy] Journal of Molecular Biology (20 February 2009) by Guy Nimrod, András Szilágyi, Christina Leslie, Nir Ben-Tal posted to bioinformatics electrostatics protein-nucleic_acid_interactions structure by sobolevnrm to the group baker-group on 2009-03-28 16:16:45 as along with 1 person reyez
	Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E [My Copy] Biophysical Chemistry, Vol. 140, No. 1-3. (March 2009), pp. 16-23. by O. Szklarczyk, J. Zuberek, J. Antosiewicz posted to electrostatics protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2009-03-19 12:10:52 as along with 1 person and 1 group jmccammon McCammon
	pH-Responsive DNA-Binding Activity of Helicobacter pylori NikR† [My Copy] Biochemistry, Vol. 48, No. 11. (24 March 2009), pp. 2486-2496. by Yanjie Li, Deborah B. Zamble posted to metalloregulation nikr pka protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2009-03-19 12:08:30 as
	Protein Sliding along DNA: Dynamics and Structural Characterization [My Copy] Journal of Molecular Biology, Vol. 385, No. 4. (30 January 2009), pp. 1087-1097. by O. Givaty, Y. Levy posted to diffusion protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2009-03-18 11:22:43 as along with 2 people barry reyez
	Helicobacter pylori NikR’s Interaction with DNA: A Two-Tiered Mode of Recognition† [My Copy] Biochemistry, Vol. 48, No. 3. (27 January 2009), pp. 527-536. by Nuvjeevan S. Dosanjh, Abby L. West, Sarah L. Michel posted to metalloregulation nikr protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2009-03-03 15:58:19 as
	Chapter 4 Modeling Protein–Protein and Protein–Nucleic Acid Interactions: Structure, Thermodynamics, and Kinetics [My Copy] Annual Reports in Computational Chemistry, Vol. 4 (2008), pp. 67-87. by H. Zhou, S. Qin, H. Tjong posted to diffusion kinetics protein-nucleic_acid_interactions protein-protein_interactions review by sobolevnrm to the group baker-group on 2009-02-18 12:31:58 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study [My Copy] Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. 4634-4645. by Johan H. Bredenberg, Cristina Russo, Marcia O. Fenley posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-07-25 11:56:28 as along with 1 person and 2 groups barry McCammon structural_bioinformatics
	DNA Binding and Bending by HMG Boxes: Energetic Determinants of Specificity [My Copy] Journal of Molecular Biology, Vol. 343, No. 2. (15 October 2004), pp. 371-393. by Anatoly I. Dragan, Christopher M. Read, Elena N. Makeyeva, et al.Ekaterina I. Milgotina, Mair E. Churchill, Colyn Crane-Robinson, Peter L. Privalov posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-06-30 15:33:24 as
	RNA recognition motifs: boring? Not quite [My Copy] Current Opinion in Structural Biology In Nucleic acids / Sequences and topology, Vol. 18, No. 3. (June 2008), pp. 290-298. by Antoine Cléry, Markus Blatter, Frédéric H. Allain posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-06-17 12:11:28 as
	Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry [My Copy] 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 to the group baker-group on 2008-04-29 11:22:51 as along with 5 people balewis jinghu_fandm kaarsinogen sunhwan marck
	Do water molecules mediate protein-DNA recognition? [My Copy] J Mol Biol, Vol. 314, No. 3. (30 November 2001), pp. 619-632. by C. K. Reddy, A. Das, B. Jayaram posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-04-25 16:07:15 as along with 2 people yoonk medic0747
	Hydration and DNA Recognition by Homeodomains [My Copy] Cell, Vol. 85, No. 7. (28 June 1996), pp. 1057-1065. by Martin Billeter, Peter Güntert, Peter Luginbühl, Kurt Wüthrich posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-04-25 15:57:42 as
	Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator [My Copy] 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 to the group baker-group on 2008-04-25 15:52:31 as
	Structural basis for gate-DNA recognition and bending by type IIA topoisomerases [My Copy] Nature, Vol. 450, No. 7173., pp. 1201-1205. by Ken C. Dong, James M. Berger posted to apbs protein-nucleic_acid_interactions structure by sobolevnrm to the group baker-group on 2008-04-18 14:02:38 as along with 1 person cactus
	Dynamics of Recognition between tRNA and Elongation Factor Tu [My Copy] 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 to the group baker-group on 2008-03-25 11:14:58 as along with 1 person jeargle
	Molecular dynamics simulations of nucleic acid-protein complexes. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 194-199. by A. D. Mackerell, L. Nilsson posted to molecular_dynamics molecular_simulation protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-03-14 11:15:30 as along with 4 people flbarroso ruvido zwang phoenixzxl
	Formation of a Wrapped DNA-Protein Interface: Experimental Characterization and Analysis of the Large Contributions of Ions and Water to the Thermodynamics of Binding IHF to H' DNA [My Copy] Journal of Molecular Biology, Vol. 377, No. 1. (14 March 2008), pp. 9-27. by Vander, Ruth M. Saecker, Record posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-03-03 12:04:18 as
	Prediction of Salt and Mutational Effects on the Association Rate of U1A Protein and U1 Small Nuclear RNA Stem/Loop II† [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 19. (1 May 2008), pp. 5955-5960. by Sanbo Qin, Huan-Xiang Zhou posted to diffusion kinetics protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-01-30 12:33:48 as
	From “Simple” DNA-Protein Interactions to the Macromolecular Machines of Gene Expression [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 36 (2007), pp. 79-105. by P. H. von Hippel posted to protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-08-06 14:33:02 as
	Dynamic Structural Rearrangements Between DNA Binding Modes of E. coli SSB Protein [My Copy] Journal of Molecular Biology, Vol. 369, No. 5. (2007), pp. 1244-57. by R. Roy, A. G. Kozlov, T. M. Lohman, T. Ha posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-07-23 13:34:53 as
	Linkage of pH, Anion and Cation Effects in Protein-Nucleic Acid Equilibria [My Copy] Journal of Molecular Biology, Vol. 236, No. 1. (1994), pp. 165-78. by L. B. Overman, T. M. Lohman posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as
	A Highly Salt-Dependent Enthalpy Change for Escherichia coli SSB Protein-Nucleic Acid Binding Due to Ion-Protein Interactions [My Copy] Biochemistry, Vol. 35, No. 16. (1996), pp. 5272-9. by T. M. Lohman, L. B. Overman, M. E. Ferrari, A. G. Kozlov posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as
	Calorimetric studies of E. coli SSB protein-single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy [My Copy] Journal of Molecular Biology, Vol. 278, No. 5. (1998), pp. 999-1014. by A. G. Kozlov, T. M. Lohman posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as
	The Importance of Coulombic End Effects: Experimental Characterization of the Effects of Oligonucleotide Flanking Charges on the Strength and Salt Dependence of Oligocation (L8+) Binding to Single-Stranded DNA Oligomers [My Copy] Biophysical Journal, Vol. 76, No. 2. (1999), pp. 1008-17. by W. Zhang, H. Ni, M. W. Capp, C. F. Anderson, T. M. Lohman, M. T. Record posted to solvation protein-nucleic_acid_interactions nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as
	RNA-binding proteins: modular design for efficient function [My Copy] Nature Reviews Molecular Cell Biology, Vol. 8, No. 6. (2007), pp. 479-90. by B. M. Lunde, C. Moore, G. Varani posted to structure protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-06-05 13:06:49 as
	Water mediated protein-DNA interactions: The relationship of thermodynamics to structural detail [My Copy] Protein Science, Vol. 5, No. 10. (1996), pp. 2115-8. by C. J. Morton, J. E. Ladbury posted to solvation protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:37:06 as
	Do electrostatic interactions destabilize protein-nucleic acid binding? [My Copy] Biopolymers (in press) by S. Qin, H. X. Zhou posted to protein-nucleic_acid_interactions nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as
	Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics [My Copy] Current Opinion in Structural Biology, Vol. 17, No. 1. (2007), pp. 87-95. by K. P. Hopfner, J. Michaelis posted to protein-nucleic_acid_interactions nucleic_acids helicase by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as
	DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces [My Copy] Nucleic Acids Research (in press) by H. Tjong, H. X. Zhou posted to protein-nucleic_acid_interactions bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as
	A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors [My Copy] Science, Vol. 315, No. 5809. (2007), pp. 233-7. by S. J. Maerkl, S. R. Quake posted to systems_biology protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as
	Fly-Casting in Protein-DNA Binding: Frustration between Protein Folding and Electrostatics Facilitates Target Recognition [My Copy] Journal of the American Chemical Society (in press) by Y. Levy, J. N. Onuchic, P. G. Wolynes posted to protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as
	Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 44. (2006), pp. 16236-41. by G. Arya, T. Schlick posted to protein-nucleic_acid_interactions multiscale by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as
	Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for `"`Chi`"` recognition complexes [My Copy] Journal of Molecular Biology, Vol. 362, No. 1. (2006), pp. 26-43. by C. J. Wong, R. L. Rice, T. Ju, T. M. Lohman posted to protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as
	Do Collective Atomic Fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A-RNA Complex [My Copy] Journal of the American Chemical Society, Vol. 128, No. 28. (2006), pp. 8992-3. by B. L. Kormos, A. M. Baranger, D. L. Beveridge posted to protein-nucleic_acid_interactions nucleic_acids molecular_dynamics allostery by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as
	Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 26. (2006), pp. 9879-84. by D. Swigon, B. D. Coleman, W. K. Olson posted to protein-nucleic_acid_interactions multiscale by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as
	Computational redesign of endonuclease DNA binding and cleavage specificity [My Copy] Nature, Vol. 441, No. 7093. (2006), pp. 656-9. by J. Ashworth, J. J. Havranek, C. M. Duarte, et al.D. Sussman, Jr, B. L. Stoddard, D. Baker posted to protein_engineering protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as
	Kinetic mechanism of adenine nucleotide binding to and hydrolysis by the Escherichia coli Rep monomer. 2. Application of a kinetic competition approach [My Copy] Biochemistry, Vol. 33, No. 48. (1994), pp. 14565-78. by K. J. M. Moore, T. M. Lohman posted to protein-nucleic_acid_interactions nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as
	Microsecond Dynamics of ProteinâDNA Interactions: Direct Observation of the Wrapping/Unwrapping Kinetics of Single-stranded DNA around the E. coli SSB Tetramer [My Copy] Journal of Molecular Biology, Vol. 359, No. 1. (2006), pp. 55-65. by S. V. Kuznetsov, A. G. Kozlov, T. M. Lohman, A. Ansari posted to protein-nucleic_acid_interactions diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as
	Effects of Monovalent Anions on a Temperature-Dependent Heat Capacity Change for Escherichia coli SSB Tetramer Binding to Single-Stranded DNA [My Copy] Biochemistry, Vol. 45, No. 16. (2006), pp. 5190-205. by A. G. Kozlov, T. M. Lohman posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:22:45 as
	Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent Approach [My Copy] Journal of the American Chemical Society, Vol. 127, No. 31. (2005), pp. 11125-31. by J. Trylska, J. A. Mccammon, Iii posted to ribosome protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:19:28 as
	The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA [My Copy] Nucleic Acids Research, Vol. 34, No. 1. (2006), pp. 275-85. by M. J. Law, M. E. Linde, E. J. Chambers, et al.C. Oubridge, P. S. Katsamba, L. Nilsson, I. S. Haworth, Laird I. A. Offringa posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:19:28 as
	Kernel-based machine learning protocol for predicting DNA-binding proteins [My Copy] Nucleic Acids Research, Vol. 33, No. 20. (2005), pp. 6486-93. by N. Bhardwaj, R. E. Langlois, H. Lu posted to protein-nucleic_acid_interactions electrostatics bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:19:26 as
	Repetitive shuttling of a motor protein on DNA [My Copy] Nature, Vol. 437, No. 7063. (2005), pp. 1321-5. by S. Myong, I. Rasnik, C. Joo, T. M. Lohman, T. Ha posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:19:03 as
	Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA [My Copy] Physical Review E, Vol. 72 (2005) by T. Ambjã¶rnsson, R. Metzler posted to statistical_mechanics protein-nucleic_acid_interactions nucleic_acids diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:18:44 as
	Energetics of DNA End Binding by E. coli RecBC and RecBCD Helicases Indicate Loop Formation in the 3â²-Single-stranded DNA Tail [My Copy] Journal of Molecular Biology, Vol. 352, No. 4. (2005), pp. 765-82. by C. J. Wong, A. L. Lucius, T. M. Lohman posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:18:25 as

Note: You may cite this page as: http://www.citeulike.org/group/2608/tag/protein-nucleic_acid_interactions

Result page: 1 2 3 Next

electrostatics	24
solvation	14
diffusion	10
nucleic_acids	8
structure	6
allostery	4
bioinformatics	4
kinetics	4
metalloregulation	4
nikr	4
review	4
apbs	2
graph_theory	2
molecular_dynamics	2
molecular_simulation	2
optimization	2
pka	2
protein-protein_interactions	2

Group: baker-group - with tag protein-nucleic_acid_interactions [104 articles] Export

Related Tags