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Tag protein_dna [38 articles]

Recent papers classified by the tag protein_dna.
  • Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
    Nucleic Acids Res, Vol. 29, No. 13. (1 July 2001), pp. 2860-2874.
    by NM Luscombe, RA Laskowski, JM Thornton
    posted to protein_dna protein_structure by shantanu on 2006-02-07 18:32:29 as ** along with 1 person and 8 groups medic0747 structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Insights into Protein–DNA Interactions through Structure Network Analysis
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000170.
    by R Sathyapriya, MS Vijayabaskar, Saraswathi Vishveshwara
    posted to protein_structure protein_dna physics molecular_mechanics by hmk on 2008-09-05 16:28:42 as ** along with 7 people and 1 group Zephyrus Ema emptyhb aalibes AbnerCYH Totobox zwang Roswell Cancer Crosstalk
  • Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study
    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 McCammon on 2008-08-29 19:08:02 as *** along with 1 person and 2 groups sobolevnrm baker-group structural_bioinformatics
  • Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 3, No. 5. (1 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 5 people and 1 group dpollard medic0747 GustavoLacerda mircea marti EisenLab
  • A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
    Nature Biotechnology, Vol. 23, No. 8. (24 July 2005), pp. 988-994.
    by Xiangdong Meng, Michael H Brodsky, Scot A Wolfe
    posted to transcription_factors protein_dna paper by aalibes on 2008-10-17 11:11:02 as ** along with 1 person and 1 group ajarman Jarman Lab
  • Structural and Thermodynamic Basis for Enhanced DNA Binding by a Promiscuous Mutant EcoRI Endonuclease.
    Structure, Vol. 15, No. 11. (November 2007), pp. 1368-1382.
    by PJ Sapienza, JM Rosenberg, L Jen-Jacobson
    posted to protein_dna by aalibes on 2007-11-14 11:41:16 as **
  • Ab initio prediction of transcription factor binding sites.
    Pac Symp Biocomput (2007), pp. 484-495.
    by LA Liu, JS Bader
    posted to protein_dna by aalibes on 2008-07-24 15:42:21 as ** along with 1 person idonaldson
  • DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
    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
  • Genome-Wide Mapping of in Vivo Protein-DNA Interactions
    Science (31 May 2007), 1141319.
    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 19 people and 5 groups 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
  • Three-dimensional intricacies in protein-DNA recognition and transcriptional control
    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 **
  • Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
    Proceedings of the National Academy of Sciences of the United States of America (30 October 2008)
    by María, Jesús Prieto, Pilar Redondo, Alejandro DD Nadra, Andreu Alibes, Luis Serrano, Sylvestre Grizot, Philippe Duchateau, Frédéric Pâques, Francisco JJ Blanco, Guillermo Montoya
    posted to protein_dna meganucleases by aalibes on 2008-11-01 21:51:38 as read
  • Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments.
    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
  • Weight matrices for protein-DNA binding sites from a single co-crystal structure.
    Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 73, No. 6 Pt 1. (June 2006)
    by RG Endres, NS Wingreen
    posted to protein_dna by aalibes on 2008-07-24 16:01:11 as **
  • Protein-DNA binding specificity predictions with structural models
    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
  • Connecting protein structure with predictions of regulatory sites.
    Proc Natl Acad Sci U S A (16 April 2007)
    by Alexandre V V Morozov, Eric D D Siggia
    posted to protein_dna transcription_factors by aalibes on 2007-05-17 15:09:20 as ** along with 4 people and 2 groups ana kaarsinogen johncumbers lusk structural_bioinformatics Bioinformatics
  • An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure.
    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 **
  • Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure.
    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 1 person medic0747
  • Precise physical models of protein-DNA interaction from high-throughput data
    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
  • Energetics of the protein-DNA-water interaction
    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
  • Visualizing one-dimensional diffusion of proteins along DNA
    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 **
  • Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification
    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
  • Protein-DNA recognition patterns and predictions.
    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 2 people ramensky medic0747
  • What Drives Proteins into the Major or Minor Grooves of DNA?
    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 **
  • Protein-nucleic acid complexes: large, small, old, and new
    Current Opinion in Structural Biology, 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 **
  • A simple physical model for the prediction and design of protein-DNA interactions.
    J Mol Biol, Vol. 344, No. 1. (12 November 2004), pp. 59-70.
    by JJ Havranek, CM Duarte, D Baker
    posted to protein_dna by aalibes on 2006-10-11 14:03:42 as ** along with 2 people kaarsinogen medic0747
  • Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.
    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
  • Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study
    Proteins: Structure, Function, and Bioinformatics, Vol. 73, No. 2. (2008), pp. 325-337.
    by Katarina Hart, Lennart Nilsson
    posted to transcription_factors protein_dna by aalibes on 2008-11-07 16:13:10 as **
  • Prediction of DNA-binding residues from sequence
    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
  • A Feature-Based Approach to Modeling Protein–DNA Interactions
    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
  • DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
    Nucl. Acids Res. (31 May 2008), gkn332.
    by Mu Gao, Jeffrey Skolnick
    posted to protein_dna by aalibes on 2008-06-02 11:25:11 as ** along with 4 people yoonk aramesh2 reyez suffer3
  • Prediction of TF target sites based on atomistic models of protein-DNA complexes
    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 transcription_factors protein_dna by aalibes on 2008-10-22 09:16:34 as ** along with 1 person lptolik
  • Spatial effects on the speed and reliability of protein-DNA search
    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 **
  • Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
    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.
    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 1 person guhjy
  • Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI
    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
  • Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
    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
  • ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by MD Kumar, KA Bava, MM Gromiha, 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
  • Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes.
    Structure (London, England : 1993), Vol. 14, No. 3. (March 2006), pp. 555-565.
    by JS Lamoureux, JN Glover
    posted to protein_dna by aalibes on 2008-07-29 12:22:00 as **
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