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kaarsinogens dna_binding [58 articles]

Neue Publikationen in kaarsinogens Bibliothek eingetragen unter dem Bezeichner: dna_binding. You can also see everyone's dna_binding.
  • 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 protein-dna_interaction machine_learning dna_binding by kaarsinogen on 2008-08-12 18:54:34 as **
  • 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 **
  • 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 chrn aalibes GustavoLacerda
  • 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 ***
  • 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
  • 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 jonsta247 chrn
  • 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
  • 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 **
  • 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 **
  • 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 **
  • 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 bpcusack eckart_bindewald cdeane
  • 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 **
  • 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 ***
  • 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
  • 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 ***
  • 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
  • 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 xili03 koller
  • Discovery of novel transcription factor binding sites by statistical overrepresentation.
    Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5549-5560.
    by S Sinha, M Tompa
    posted to dna_binding e_coli transcription_factor by kaarsinogen on 2006-07-17 22:44:59 as ** along with 9 people pradiptaray wenhan ep161302 dquest xiaobeizhao smiddha GeeSharpMinor xi03 xili03
  • 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 sconlan LeightonP
  • 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 3 people and 1 group jjray discreteonyxorb cisevol cis-regulatory-evolution
  • 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
  • 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 **
  • 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 8 people jonsta247 dquest kristallreiner miguel johncumbers tvdbulck epigenetics yevishere
  • 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 aalibes lusk Stew nklee yevishere xili03 EisenLab
  • 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
  • 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 **
  • Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity
    Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59.
    by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale
    posted to 2005_2006_dnabp dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-01-30 19:48:04 as ***** along with 13 people and 5 groups emptyhb Terkko tuck brant xwbcn dchughes nickluscombe olympos cabbagezs karfunkel maximilianh heliopais oelemento Bioinformatics EisenLab G4ID EBI-regulation Genetics-of-Gambling
  • 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 10 people and 1 group bozdagd maralena jfr balajis tabu vega kengg jackjackjjj jtomasch karfunkel Plantandetc
  • 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
  • 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
  • Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?
    J Mol Biol, Vol. 301, No. 3. (18 August 2000), pp. 597-624.
    by CO Pabo, L Nekludova
    posted to dna_binding docking protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 23:30:10 as ** along with 1 person medic0747
  • 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
  • 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
  • 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
  • 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
  • Consistencies of individual DNA base-amino acid interactions in structures and sequences.
    Nucleic Acids Res, Vol. 23, No. 22. (25 November 1995), pp. 4707-4711.
    by B Lustig, RL Jernigan
    posted to dna_binding protein-dna_interaction protein_descriptors protein_structure by kaarsinogen on 2006-01-25 22:32:32 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 dna_binding protein-dna_interaction by kaarsinogen on 2006-01-25 22:25:52 as ** along with 2 people aalibes medic0747
  • Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence.
    Biochim Biophys Acta, Vol. 1648, No. 1-2. (30 May 2003), pp. 127-133.
    by YD Cai, SL Lin
    posted to dna_binding protein_descriptors svm by kaarsinogen on 2006-01-25 19:13:32 as read
  • 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
  • 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 wenhan balajis nklee
  • 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 *****
  • 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 **
  • 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
  • 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
  • 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
  • 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 5 people mbj dquest lusk ezralanglois xili03
  • 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 ***
  • 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
  • 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 emptyhb dpollard lusk cisevol EisenLab cis-regulatory-evolution
  • 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 ***
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