Tag protein_dna [47 articles] Export

Recent papers classified by the tag protein_dna.

	Energetics of protein-DNA interactions. [My Copy] Nucleic acids research, Vol. 35, No. 4. (February 2007), pp. 1039-1047. by Jason E. Donald, William W. Chen, Eugene I. Shakhnovich posted to protein_dna by aalibes on 2009-10-30 13:18:36 as along with 1 person oteri
	Crystal Structure of E47−NeuroD1/Beta2 bHLH Domain−DNA Complex: Heterodimer Selectivity and DNA Recognition†,‡ [My Copy] Biochemistry, Vol. 47, No. 1. (1 January 2008), pp. 218-229. by Antonella Longo, Gerald P. Guanga, Robert B. Rose posted to protein_dna bhlh by aalibes on 2009-10-09 10:39:14 as
	Comparison of DNA binding across protein superfamilies [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Bruno Contreras-Moreira, Javier Sancho, Vladimir E. Angarica posted to protein_dna by aalibes on 2009-09-07 10:33:17 as along with 1 person dimka
	Motif-directed flexible backbone design of functional interactions [My Copy] Protein Science, Vol. 18, No. 6. (2009), pp. 1293-1305. by James J. Havranek, David Baker posted to protein_dna protein_engineering by aalibes on 2009-06-05 15:25:11 as along with 1 person anna_yershova
	Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 176. by Jiajian Liu, Gary Stormo posted to protein_dna by aalibes on 2009-05-20 10:30:59 as
	Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. [My Copy] Nucleic acids research, Vol. 37, No. 12. (1 July 2009), pp. 4076-4088. by N. Alpay Temiz, Carlos J. Camacho posted to protein_dna by aalibes on 2009-05-18 11:10:14 as along with 1 person maximilianh
	Assessment of the optimization of affinity and specificity at protein-DNA interfaces. [My Copy] Nucleic acids research (23 April 2009) by Justin Ashworth, David Baker posted to protein_dna by aalibes on 2009-04-28 12:15:43 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 bd_simulation protein_dna by barry on 2009-03-25 21:27:28 as along with 2 people and 1 group sobolevnrm reyez baker-group
	Additivity in protein-DNA interactions: how good an approximation is it? [My Copy] Nucleic Acids Res, Vol. 30, No. 20. (15 October 2002), pp. 4442-4451. by P. V. Benos, M. L. Bulyk, G. D. Stormo posted to protein_dna by aalibes on 2009-03-12 12:28:56 as along with 4 people erdos medic0747 emptyhb yevishere
	Systematic prediction of control proteins and their DNA binding sites [My Copy] Nucl. Acids Res., Vol. 37, No. 2. (1 February 2009), pp. 441-451. by Valeriy Sorokin, Konstantin Severinov, Mikhail S. Gelfand posted to protein_dna by aalibes on 2009-02-09 12:00:23 as
	Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 73, No. 2. (2008), pp. 325-337. by Katarina Hart, Lennart Nilsson posted to protein_dna transcription_factors by aalibes on 2008-11-07 16:13:10 as
	Prediction of TF target sites based on atomistic models of protein-DNA complexes [My Copy] BMC Bioinformatics, Vol. 9 (16 October 2008), 436. by Vladimir E. Angarica, Abel G. Perez, Ana T. Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira posted to protein_dna transcription_factors by aalibes on 2008-10-22 09:16:34 as along with 2 people emptyhb lptolik
	A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors [My Copy] Nature Biotechnology, Vol. 23, No. 8. (24 July 2005), pp. 988-994. by Xiangdong Meng, Michael H. Brodsky, Scot A. Wolfe posted to paper protein_dna transcription_factors by aalibes on 2008-10-17 11:11:02 as along with 3 people and 1 group austin_mcdonald jbhiatt ajarman Jarman Lab
	Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins [My Copy] Nucl. Acids Res. (18 September 2008), gkn573. by Shandar Ahmad, Ozlem Keskin, Akinori Sarai, Ruth Nussinov posted to protein_dna by aalibes on 2008-10-13 12:08:59 as along with 2 people TOchi maximilianh
	UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. [My Copy] Nucleic acids research (8 October 2008) by Daniel E E. Newburger, Martha L L. Bulyk posted to protein_dna by aalibes on 2008-10-13 08:54:31 as along with 2 people lptolik guhjy
	Insights into Protein–DNA Interactions through Structure Network Analysis [My Copy] PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000170. by R. Sathyapriya, M. S. Vijayabaskar, Saraswathi Vishveshwara posted to protein_dna by aalibes on 2008-09-10 15:03:07 as along with 9 people and 1 group TRHvidsten svozil Zephyrus Ema emptyhb AbnerCYH Totobox zwang hmk Roswell Cancer Crosstalk
	Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification [My Copy] Structure, Vol. 16, No. 9. (10 September 2008), pp. 1407-1416. by Michael M. Brent, Ruchi Anand, Ronen Marmorstein posted to protein_dna by aalibes on 2008-09-10 14:53:07 as along with 1 person guhjy
	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_dna solvation by barry to the group structural_bioinformatics on 2008-08-29 19:08:02 as along with 1 person and 2 groups sobolevnrm baker-group McCammon
	Visualizing one-dimensional diffusion of proteins along DNA [My Copy] Nature Structural & Molecular Biology, Vol. 15, No. 8. (05 August 2008), pp. 768-774. by Jason Gorman, Eric C. Greene posted to protein_dna by aalibes on 2008-08-29 15:33:27 as
	A Feature-Based Approach to Modeling Protein–DNA Interactions [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000154. by Eilon Sharon, Shai Lubliner, Eran Segal posted to protein_dna transcription_factors by aalibes on 2008-08-28 15:51:00 as along with 5 people ptrobajo dakelley Stew emptyhb zwang
	Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes. [My Copy] Structure (London, England : 1993), Vol. 14, No. 3. (March 2006), pp. 555-565. by J. S. Lamoureux, J. N. Glover posted to protein_dna by aalibes on 2008-07-29 12:22:00 as
	Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. [My Copy] Journal of computational biology : a journal of computational molecular cell biology (23 July 2008) by Anthony A A. Philippakis, Aaron M M. Qureshi, Michael F F. Berger, Martha L L. Bulyk posted to protein_dna by aalibes on 2008-07-28 10:13:49 as along with 1 person guhjy
	Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. [My Copy] Nucleic Acids Res (5 November 2007) by Buyong Ma, Arnold J J. Levine posted to cancer p53 protein_dna by aalibes on 2008-07-25 11:34:04 as along with 1 person oelemento
	Weight matrices for protein-DNA binding sites from a single co-crystal structure. [My Copy] Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 73, No. 6 Pt 1. (June 2006) by R. G. Endres, N. S. Wingreen posted to protein_dna by aalibes on 2008-07-24 16:01:11 as
	Protein-DNA recognition patterns and predictions. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 34 (2005), pp. 379-398. by A. Sarai, H. Kono posted to protein_dna by aalibes on 2008-07-24 15:43:07 as along with 3 people svozil ramensky medic0747
	Ab initio prediction of transcription factor binding sites. [My Copy] Pac Symp Biocomput (2007), pp. 484-495. by L. A. Liu, J. S. Bader posted to protein_dna by aalibes on 2008-07-24 15:42:21 as along with 1 person idonaldson
	Three-dimensional intricacies in protein-DNA recognition and transcriptional control [My Copy] Nature Structural & Molecular Biology, Vol. 14, No. 12., pp. 1118-1119. by Stephen C. Harrison posted to protein_dna by aalibes on 2008-07-24 15:40:19 as
	Protein-DNA binding specificity predictions with structural models [My Copy] Nucleic Acids Research, Vol. 33, No. 18. (2005), pp. 5781-5798. by Alexandre V. Morozov, James J. Havranek, David Baker, Eric D. Siggia posted to protein_dna by aalibes on 2008-07-10 14:03:15 as along with 1 person medic0747
	Spatial effects on the speed and reliability of protein-DNA search [My Copy] Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), pp. 3570-3578. by Zeba Wunderlich, Leonid A. Mirny posted to protein_dna by aalibes on 2008-06-26 10:48:26 as
	DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions [My Copy] Nucl. Acids Res., Vol. 36, No. 12. (1 July 2008), pp. 3978-3992. by Mu Gao, Jeffrey Skolnick posted to protein_dna by aalibes on 2008-06-02 11:25:11 as along with 5 people operon yoonk aramesh2 reyez suffer3
	Protein-nucleic acid complexes: large, small, old, and new [My Copy] Current Opinion in Structural Biology In Folding and Binding / Protein-nucleic acid interactions, Vol. 18, No. 1. (February 2008), pp. 67-69. by Gregory D. Van Duyne, Wei Yang posted to protein_dna by aalibes on 2008-02-20 15:13:46 as
	Structural and Thermodynamic Basis for Enhanced DNA Binding by a Promiscuous Mutant EcoRI Endonuclease. [My Copy] Structure, Vol. 15, No. 11. (November 2007), pp. 1368-1382. by P. J. Sapienza, J. M. Rosenberg, L. Jen-Jacobson posted to protein_dna by aalibes on 2007-11-14 11:41:16 as
	Prediction of DNA-binding residues from sequence [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i347-353. by Yanay Ofran, Venkatesh Mysore, Burkhard Rost posted to protein_dna by aalibes on 2007-07-24 09:25:52 as along with 3 people kaarsinogen GustavoLacerda chrn
	Genome-Wide Mapping of in Vivo Protein-DNA Interactions [My Copy] Science, Vol. 316, No. 5830. (8 June 2007), pp. 1497-1502. by David S. Johnson, Ali Mortazavi, Richard M. Myers, Barbara Wold posted to protein_dna transcription_factors by aalibes on 2007-06-08 12:10:09 as along with 24 people and 5 groups oannes daforerog tonamswish ewilban1 aprasad jo_davies balicea andersbj JeremyZucker aswin kengg giovanni cjeans ghattem zwang epigenetics biomcgary george_g cabbagezs Jporci blobbybirdman caseybrown emptyhb dquest Bioinformatics microRNA Marcotte_Lab UH - Computational Biology Myxo group
	DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e61. by Shaun Mahony, Philip E. Auron, Panayiotis V. Benos posted to protein_dna by aalibes on 2007-05-25 09:12:22 as along with 4 people zwang nklee heliopais pradiptaray
	Connecting protein structure with predictions of regulatory sites [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7068-7073. by Alexandre V. Morozov, Eric D. Siggia posted to protein_dna transcription_factors by aalibes on 2007-05-17 15:09:20 as along with 7 people and 2 groups vingron nklee maximilianh ana kaarsinogen johncumbers lusk structural_bioinformatics Bioinformatics
	Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites [My Copy] PLoS Comput Biol, Vol. 3, No. 5. (11 May 2007), e90. by Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich posted to protein_dna transcription_factors by aalibes on 2007-05-11 15:57:47 as along with 7 people and 1 group pradiptaray nklee dpollard medic0747 GustavoLacerda mircea marti EisenLab
	Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. [My Copy] Nucleic Acids Res (30 January 2007) by Trevor W W. Siggers, Barry Honig posted to protein_dna zinc_fingers by aalibes on 2007-04-25 09:33:12 as along with 1 person and 1 group dpollard EisenLab
	Energetics of the protein-DNA-water interaction [My Copy] BMC Structural Biology, Vol. 7 (10 January 2007), 4. by Francesca Spyrakis, Pietro Cozzini, Chiara Bertoli, Anna Marabotti, Glen E. Kellogg, Andrea Mozzarelli posted to protein_dna by aalibes on 2007-03-06 14:34:28 as along with 3 people medic0747 Ema jjray
	Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI [My Copy] Journal of Molecular Biology, Vol. 329, No. 2. (30 May 2003), pp. 253-269. by Brett Chevalier, Monique Turmel, Claude Lemieux, Raymond J. Monnat, Barry L. Stoddard posted to protein_dna by aalibes on 2007-02-15 17:20:34 as along with 1 person Bobbi
	Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure. [My Copy] Proteins, Vol. 61, No. 2. (1 November 2005), pp. 258-271. by D. Lejeune, N. Delsaux, B. Charloteaux, A. Thomas, R. Brasseur posted to protein_dna by aalibes on 2007-02-15 13:48:09 as along with 3 people and 1 group kaarsinogen svozil medic0747 Bioinformatics
	Precise physical models of protein-DNA interaction from high-throughput data [My Copy] PNAS, Vol. 104, No. 2. (9 January 2007), pp. 501-506. by Justin B. Kinney, Gasper Tkacik, Curtis G. Callan posted to protein_dna by aalibes on 2007-01-10 08:58:54 as along with 2 people zwang emptyhb
	What Drives Proteins into the Major or Minor Grooves of DNA? [My Copy] Journal of Molecular Biology, Vol. 365, No. 1. (5 January 2007), pp. 1-9. by Peter L. Privalov, Anatoly I. Dragan, Colyn Crane-Robinson, Kenneth J. Breslauer, David P. Remeta, Conceicao A. Minetti posted to protein_dna by aalibes on 2006-12-01 11:58:15 as
	An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. [My Copy] Proteins (31 October 2006) by Timothy A A. Robertson, Gabriele Varani posted to protein_dna by aalibes on 2006-11-07 09:07:25 as
	ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. [My Copy] Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) by M. D. Kumar, K. A. Bava, M. M. Gromiha, et al.P. Prabakaran, K. Kitajima, H. Uedaira, A. Sarai posted to protein_dna by aalibes on 2006-10-16 10:58:51 as along with 3 people and 1 group massivemayhem cat_worth gisle structural_bioinformatics
	A simple physical model for the prediction and design of protein-DNA interactions. [My Copy] J Mol Biol, Vol. 344, No. 1. (12 November 2004), pp. 59-70. by J. J. Havranek, C. M. Duarte, D. Baker posted to protein_dna by aalibes on 2006-10-11 14:03:42 as along with 2 people kaarsinogen medic0747
	Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. [My Copy] Nucleic Acids Res, Vol. 29, No. 13. (1 July 2001), pp. 2860-2874. by N. M. Luscombe, R. A. Laskowski, J. M. Thornton posted to protein_structure protein_dna by shantanu to the group microRNA on 2006-02-07 18:32:29 as along with 3 people and 7 groups kaarsinogen semin medic0747 structural_bioinformatics MathBio Biostatistics Bioinformatics Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology

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Tag protein_dna [47 articles] Export

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