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タグ: dna_binding [70 articles]

Recent papers classified by the tag dna_binding.
  • Functional analysis of the adenovirus type 5 DNA-binding protein: site-directed mutants which are defective for adeno-associated virus helper activity.
    J Virol, Vol. 60, No. 2. (November 1986), pp. 653-661.
    by CO Quinn, GR Kitchingman
    posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:26:36 as **
  • Identification of the binding sites of regulatory proteins in bacterial genomes.
    Proc Natl Acad Sci U S A, Vol. 99, No. 18. (3 September 2002), pp. 11772-11777.
    by H Li, V Rhodius, C Gross, ED Siggia
    posted to dna_binding genome by kaarsinogen on 2005-10-07 20:02:41 as ** along with 1 person dquest
  • PSSM-based prediction of DNA binding sites in proteins.
    BMC Bioinformatics, Vol. 6 (2005)
    by S Ahmad, A Sarai
    posted to 2005_2006_dnabp dna_binding protein-dna_interaction pssm by kaarsinogen on 2006-11-03 23:08:37 as ***
  • DNA binding sites: representation and discovery.
    Bioinformatics, Vol. 16, No. 1. (January 2000), pp. 16-23.
    by GD Stormo
    posted to dna_binding by kaarsinogen on 2005-11-04 20:37:37 as *** along with 7 people emptyhb isimpson mbj dquest lusk ezralanglois xili03
  • Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
    J Mol Biol, Vol. 320, No. 5. (26 July 2002), pp. 991-1009.
    by NM Luscombe, JM Thornton
    posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-01-25 23:33:55 as ** along with 1 person medic0747
  • Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by C Dieterich, R Herwig, M Vingron
    posted to signaling_pathways transcription_factor dna_binding gene by kaarsinogen on 2005-11-04 20:33:20 as ***
  • Moment-based prediction of DNA-binding proteins.
    J Mol Biol, Vol. 341, No. 1. (30 July 2004), pp. 65-71.
    by S Ahmad, A Sarai
    posted to dna_binding protein-dna_interaction by kaarsinogen on 2005-08-05 19:34:22 as ***** along with 1 person ziquje
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-26 20:41:26 as *** along with 6 people and 1 group lusk Stew nklee yevishere xili03 aalibes EisenLab
  • A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction
    Journal of Structural and Functional Genomics, Vol. 5, No. 4. (January 2005), pp. 255-265.
    by William Mclaughlin, Daniel Kulp, Joanna Cruz, Xiang-Jun Lu, Catherine Lawson, Helen Berman
    posted to protein_structure protein-dna_interaction dna_binding by kaarsinogen on 2007-01-22 06:42:38 as **
  • Protein-DNA interactions: A structural analysis.
    J Mol Biol, Vol. 287, No. 5. (16 April 1999), pp. 877-896.
    by S Jones, P van Heyningen, HM Berman, JM Thornton
    posted to dna_binding protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 22:49:03 as ** along with 1 person medic0747
  • Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites.
    Nucleic Acids Res, Vol. 26, No. 10. (15 May 1998), pp. 2306-2312.
    by Y Mandel-Gutfreund, H Margalit
    posted to dna_binding protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 22:35:43 as ** along with 2 people medic0747 roys
  • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.
    Nature, Vol. 409, No. 6819. (25 January 2001), pp. 533-538.
    by VR Iyer, CE Horak, CS Scafe, D Botstein, M Snyder, PO Brown
    posted to dna_binding genome transcription_factor by kaarsinogen on 2005-11-04 20:43:00 as read along with 1 person dquest
  • DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
    Nucl. Acids Res., Vol. 35, No. 5. (12 March 2007), pp. 1465-1477.
    by Harianto Tjong, Huan-Xiang Zhou
    posted to dna_binding machine_learning protein-dna_interaction protein_descriptors protein_structure transcription_factor by kaarsinogen on 2007-06-01 21:15:06 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 dna_binding protein-dna_interaction protein_structure transcription_factor by kaarsinogen on 2007-06-01 22:37:08 as *** along with 4 people and 2 groups ana aalibes johncumbers lusk structural_bioinformatics Bioinformatics
  • Annotating nucleic acid-binding function based on protein structure.
    J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1065-1079.
    by EW Stawiski, LM Gregoret, Y Mandel-Gutfreund
    posted to dna_binding protein-dna_interaction by kaarsinogen on 2005-11-11 19:30:49 as *****
  • Detection, Rescue, and Mapping of Mutations in the Adenovirus DNA Binding Protein Gene
    PNAS, Vol. 80, No. 6. (15 March 1983), pp. 1674-1677.
    by JC Nicolas, CSH Young, F Suarez, M Girard, AJ Levine
    posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:28:06 as **
  • rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 118-121.
    by JV Ponomarenko, TI Merkulova, GV Orlova, ON Fokin, EV Gorshkova, AS Frolov, VP Valuev, MP Ponomarenko
    posted to dna_binding protein-dna_interaction transcription transcription_factor by kaarsinogen on 2005-10-14 20:57:18 as ***
  • DNA binding sites: representation and discovery
    Bioinformatics, Vol. 16, No. 1. (1 January 2000), pp. 16-23.
    by Gary D Stormo
    posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-06-28 23:00:52 as ** along with 1 person emptyhb
  • Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.
    Nat Biotechnol, Vol. 21, No. 4. (April 2003), pp. 435-439.
    by ZS Qin, LA McCue, W Thompson, L Mayerhofer, CE Lawrence, JS Liu
    posted to bayesian_network dna_binding protein-dna_interaction by kaarsinogen on 2005-11-11 20:05:51 as ** along with 3 people balajis nklee wenhan
  • Adaptive evolution of transcription factor binding sites.
    BMC Evol Biol, Vol. 4, No. 1. (28 October 2004)
    by J Berg, S Willmann, M Lässig
    posted to dna_binding e_coli protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 19:07:37 as ** along with 4 people and 1 group bmajoros jjray discreteonyxorb cisevol cis-regulatory-evolution
  • 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 dna_binding protein-dna_interaction by kaarsinogen on 2008-03-07 19:03:24 as ** along with 3 people aalibes GustavoLacerda chrn
  • Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
    Nucleic Acids Res, Vol. 31, No. 24. (15 December 2003), pp. 7189-7198.
    by S Jones, HP Shanahan, HM Berman, JM Thornton
    posted to dna_binding electrostatic_potential by kaarsinogen on 2005-11-11 19:20:45 as ** along with 2 people medic0747 carlescorbi
  • How do site-specific DNA-binding proteins find their targets?
    Nucl. Acids Res., Vol. 32, No. 10. (3 June 2004), pp. 3040-3052.
    by Stephen E Halford, John F Marko
    posted to dna_binding protein-dna_interaction transcription_factor by kaarsinogen on 2007-06-01 21:29:15 as *** along with 2 people JintuRabha chrn
  • Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.
    BMC Bioinformatics, Vol. 5, No. 1. (17 December 2004)
    by TZ Sen, A Kloczkowski, RL Jernigan, C Yan, V Honavar, KM Ho, CZ Wang, Y Ihm, H Cao, X Gu, D Dobbs
    posted to dna_binding by kaarsinogen on 2005-11-04 20:00:06 as *** along with 1 person cjeans
  • Structural features of protein-nucleic acid recognition sites.
    Biochemistry, Vol. 38, No. 7. (16 February 1999), pp. 1999-2017.
    by K Nadassy, SJ Wodak, J Janin
    posted to dna_binding docking protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 23:39:26 as ** along with 1 person medic0747
  • Structure-based prediction of DNA target sites by regulatory proteins.
    Proteins, Vol. 35, No. 1. (1 April 1999), pp. 114-131.
    by H Kono, A Sarai
    posted to dna_binding protein-dna_interaction protein_structure transcription_factor by kaarsinogen on 2006-01-25 22:44:19 as ** along with 1 person medic0747
  • Genome-Wide Location and Function of DNA Binding Proteins
    Science, Vol. 290, No. 5500. (22 December 2000), pp. 2306-2309.
    by Bing Ren, Francois Robert, John J Wyrick, Oscar Aparicio, Ezra G Jennings, Itamar Simon, Julia Zeitlinger, Jorg Schreiber, Nancy Hannett, Elenita Kanin, Thomas L Volkert, Christopher J Wilson, Stephen P Bell, Richard A Young
    posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-28 22:54:05 as *** along with 7 people miguel johncumbers tvdbulck epigenetics yevishere kristallreiner dquest
  • Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity
    Journal of Molecular Biology, Vol. 350, No. 3. (15 July 2005), pp. 402-415.
    by Michele Raviscioni, Peili Gu, Minawar Sattar, Austin J Cooney, Olivier Lichtarge
    posted to 2005_2006_dnabp dna_binding evolution protein-dna_interaction by kaarsinogen on 2005-09-23 18:42:10 as *** along with 4 people mdimmic chrn lulab cjeans
  • Global Analysis of Protein Activities Using Proteome Chips
    Science, Vol. 293, No. 5537. (14 September 2001), pp. 2101-2105.
    by Heng Zhu, Metin Bilgin, Rhonda Bangham, David Hall, Antonio Casamayor, Paul Bertone, Ning Lan, Ronald Jansen, Scott Bidlingmaier, Thomas Houfek, Tom Mitchell, Perry Miller, Ralph A Dean, Mark Gerstein, Michael Snyder
    posted to dna_binding protein-dna_interaction protein_chips by kaarsinogen on 2006-01-23 19:46:22 as *** along with 1 person selrac
  • Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation
    Genome Res., Vol. 14, No. 1. (1 January 2004), pp. 99-108.
    by Moshe Pritsker, Yir-Chung Liu, Michael A Beer, Saeed Tavazoie
    posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:47:37 as ** along with 2 people koller xili03
  • BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by L Wang, SJ Brown
    posted to dna_binding protein-dna_interaction protein-rna by kaarsinogen on 2007-06-04 18:06:47 as ***
  • Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.
    Genome Res, Vol. 11, No. 7. (July 2001), pp. 1175-1186.
    by PF Cliften, LW Hillier, L Fulton, T Graves, T Miner, WR Gish, RH Waterston, M Johnston
    posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-28 23:05:19 as *** along with 2 people evaf nklee
  • NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
    Nucleic Acids Res, Vol. 25, No. 24. (15 December 1997), pp. 4940-4945.
    by NM Luscombe, RA Laskowski, JM Thornton
    posted to dna_binding protein-dna_interaction by kaarsinogen on 2005-09-06 20:04:33 as ***
  • DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein.
    Mol Cell Biol, Vol. 17, No. 4. (April 1997), pp. 1881-1889.
    by TB Acton, H Zhong, AK Vershon
    posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:13:45 as **
  • A global map of p53 transcription-factor binding sites in the human genome.
    Cell, Vol. 124, No. 1. (13 January 2006), pp. 207-219.
    by CL Wei, Q Wu, VB Vega, KP Chiu, P Ng, T Zhang, A Shahab, HC Yong, Y Fu, Z Weng, J Liu, XD Zhao, JL Chew, YL Lee, VA Kuznetsov, WK Sung, LD Miller, B Lim, ET Liu, Q Yu, HH Ng, Y Ruan
    posted to 2005_2006_dnabp dna_binding genome p53 protein-dna_interaction transcription_factor by kaarsinogen on 2006-01-30 19:46:35 as ***** along with 11 people and 1 group drestion jfr balajis tabu vega kengg jackjackjjj jtomasch karfunkel maralena bozdagd Plantandetc
  • notes Satisfying hydrogen bonding potential in proteins.
    J Mol Biol, Vol. 238, No. 5. (20 May 1994), pp. 777-793.
    by IK McDonald, JM Thornton
    posted to dna_binding hydrogen_bonding protein-dna_interaction by kaarsinogen on 2005-09-06 19:59:41 as *** along with 3 people bicko lna massivemayhem
  • Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces.
    Proteins, Vol. 55, No. 4. (1 June 2004), pp. 885-894.
    by Y Tsuchiya, K Kinoshita, H Nakamura
    posted to dna_binding electrostatic_potential by kaarsinogen on 2005-11-11 19:25:46 as **
  • Learning to translate sequence and structure to function: identifying DNA binding and membrane binding proteins.
    Annals of biomedical engineering, Vol. 35, No. 6. (June 2007), pp. 1043-1052.
    by RE Langlois, MB Carson, N Bhardwaj, H Lu
    posted to dna_binding machine_learning protein-dna_interaction by kaarsinogen on 2008-08-12 18:54:34 as **
  • Definition of a consensus binding site for p53.
    Nat Genet, Vol. 1, No. 1. (April 1992), pp. 45-49.
    by WS el-Deiry, SE Kern, JA Pietenpol, KW Kinzler, B Vogelstein
    posted to dna_binding p53 protein-dna_interaction by kaarsinogen on 2006-03-08 17:47:28 as **
  • Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.
    Proteins, Vol. 64, No. 1. (1 July 2006), pp. 19-27.
    by IB Kuznetsov, Z Gou, R Li, S Hwang
    posted to 2005_2006_dnabp dna_binding evolution protein-dna_interaction svm by kaarsinogen on 2006-07-29 00:36:37 as *** along with 1 person hplatero
  • A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli.
    Genome Res, Vol. 14, No. 2. (February 2004), pp. 201-208.
    by ML Bulyk, AM McGuire, N Masuda, GM Church
    posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:24:10 as ** along with 2 people LeightonP sconlan
  • A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.
    J Mol Biol, Vol. 284, No. 2. (27 November 1998), pp. 241-254.
    by K Robison, AM McGuire, GM Church
    posted to dna_binding e_coli protein-dna_interaction by kaarsinogen on 2006-01-25 22:38:11 as ** along with 1 person nklee
  • 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 dna_binding protein-dna_interaction by kaarsinogen on 2006-01-25 22:25:52 as ** along with 2 people aalibes medic0747
  • Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies.
    Proc Natl Acad Sci U S A, Vol. 102, No. 44. (1 November 2005), pp. 15936-15941.
    by V Mustonen, M Lässig
    posted to 2005_2006_dnabp dna_binding evolution population_genetics promoter by kaarsinogen on 2005-11-04 19:57:32 as *** along with 4 people and 2 groups dpollard lusk cisevol emptyhb EisenLab cis-regulatory-evolution
  • Predicting DNA-binding sites of proteins from amino acid sequence.
    BMC Bioinformatics, Vol. 7 (2006)
    by C Yan, M Terribilini, F Wu, RL Jernigan, D Dobbs, V Honavar
    posted to 2005_2006_dnabp dna_binding protein-dna_interaction protein_descriptors by kaarsinogen on 2006-11-03 20:47:02 as *** along with 3 people ameetsoni ezralanglois dandaman
  • Why are proteins so robust to site mutations?
    J Mol Biol, Vol. 315, No. 3. (18 January 2002), pp. 479-484.
    by DM Taverna, RA Goldstein
    posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:22:26 as ** along with 3 people eckart_bindewald cdeane bpcusack
  • Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions
    FEBS Letters, Vol. 581, No. 5. (6 March 2007), pp. 1058-1066.
    by Nitin Bhardwaj, Hui Lu
    posted to dna_binding protein-dna_interaction by kaarsinogen on 2008-03-07 19:15:28 as **
  • Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations.
    Science, Vol. 265, No. 5170. (15 July 1994), pp. 346-355.
    by Y Cho, S Gorina, PD Jeffrey, NP Pavletich
    posted to dna_binding p53 protein-dna_interaction by kaarsinogen on 2006-03-08 17:49:17 as read
  • Conservation of DNA curvature signals in regulatory regions of prokaryotic genes.
    Nucleic Acids Res, Vol. 31, No. 23. (1 December 2003), pp. 6770-6777.
    by R Jáuregui, C Abreu-Goodger, G Moreno-Hagelsieb, J Collado-Vides, E Merino
    posted to dna_binding protein_structure signaling_pathways transcription transcription_factor by kaarsinogen on 2006-10-02 21:19:13 as ***
  • Factors influencing the identification of transcription factor binding sites by cross-species comparison.
    Genome Res, Vol. 12, No. 10. (October 2002), pp. 1523-1532.
    by LA McCue, W Thompson, CS Carmack, CE Lawrence
    posted to dna_binding e_coli transcription_factor by kaarsinogen on 2005-11-04 20:39:29 as *** along with 2 people dquest nklee
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