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Tag protein-dna_interaction [101 articles]

Recent papers classified by the tag protein-dna_interaction.
  • An analysis of the relationship between hydration and protein-DNA interactions.
    Biophys J, Vol. 75, No. 5. (November 1998), pp. 2170-2177.
    by J Woda, B Schneider, K Patel, K Mistry, HM Berman
    posted to protein-dna_interaction by medic0747 on 2007-04-13 16:37:22 as **
  • Physical basis of a protein-DNA recognition code.
    Curr Opin Struct Biol, Vol. 7, No. 1. (February 1997), pp. 117-125.
    by Y Choo, A Klug
    posted to protein-dna_interaction by medic0747 on 2007-04-10 13:01:38 as **
  • 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 protein-dna_interaction by medic0747 on 2007-01-29 12:39:04 as ** along with 1 person kaarsinogen
  • Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition.
    Structure, Vol. 7, No. 12. (15 December 1999)
    by J Janin
    posted to protein-dna_interaction protein-protein_interaction by medic0747 on 2007-01-29 13:07:40 as **
  • Additivity in protein-DNA interactions: how good an approximation is it?
    Nucleic Acids Res, Vol. 30, No. 20. (15 October 2002), pp. 4442-4451.
    by PV Benos, ML Bulyk, GD Stormo
    posted to protein-dna_interaction by medic0747 on 2007-04-10 13:22:55 as ** along with 3 people erdos emptyhb yevishere
  • Sequence-dependent DNA structure. The role of base stacking interactions.
    J Mol Biol, Vol. 230, No. 3. (5 April 1993), pp. 1025-1054.
    by CA Hunter
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:55:22 as ** along with 1 person Elena_Zubova
  • 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_interaction by medic0747 on 2007-03-21 12:54:56 as ** along with 1 person and 8 groups shantanu structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • 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 protein-dna_interaction by medic0747 on 2007-03-21 14:39:29 as ** along with 1 person kaarsinogen
  • Adaptability at the protein-DNA interface is an important aspect of sequence recognition by bZIP proteins.
    Proc Natl Acad Sci U S A, Vol. 90, No. 10. (15 May 1993), pp. 4513-4517.
    by J Kim, D Tzamarias, T Ellenberger, SC Harrison, K Struhl
    posted to protein-dna_interaction by medic0747 on 2007-06-14 16:51:18 as **
  • 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_interaction by medic0747 on 2007-05-11 15:56:53 as ** along with 5 people and 1 group aalibes dpollard GustavoLacerda mircea marti EisenLab
  • Selection of DNA Binding Sites for Zinc Fingers Using Rationally Randomized DNA Reveals Coded Interactions
    PNAS, Vol. 91, No. 23. (8 November 1994), pp. 11168-11172.
    by Y Choo, A Klug
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:07:56 as ** along with 1 person perrywoo
  • 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_interaction by medic0747 on 2007-06-14 16:59:25 as ** along with 3 people aalibes Ema jjray
  • Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
    Nucleic Acids Res, Vol. 32, No. 16. (2004), pp. 4732-4741.
    by HP Shanahan, MA Garcia, S Jones, JM Thornton
    posted to protein-dna_interaction by medic0747 on 2007-09-26 14:03:50 as ** along with 3 people kaarsinogen sriram_s ezralanglois
  • Interaction of DNA with clusters of amino acids in proteins.
    Nucleic Acids Res, Vol. 32, No. 14. (2004), pp. 4109-4118.
    by R Sathyapriya, S Vishveshwara
    posted to protein-dna_interaction by medic0747 on 2007-04-13 16:16:26 as **
  • 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 protein-dna_interaction by medic0747 on 2007-04-03 21:34:13 as ** along with 2 people yoonk kaarsinogen
  • Using structural motif templates to identify proteins with DNA binding function.
    Nucleic Acids Res, Vol. 31, No. 11. (1 June 2003), pp. 2811-2823.
    by S Jones, JA Barker, I Nobeli, JM Thornton
    posted to protein-dna_interaction by medic0747 on 2007-09-26 14:57:22 as ** along with 1 person chrn
  • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles.
    J Mol Biol, Vol. 253, No. 2. (20 October 1995), pp. 370-382.
    by Y Mandel-Gutfreund, O Schueler, H Margalit
    posted to protein-dna_interaction by medic0747 on 2007-03-20 15:29:54 as **
  • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.
    Proc Natl Acad Sci U S A, Vol. 98, No. 13. (19 June 2001), pp. 7158-7163.
    by ML Bulyk, X Huang, Y Choo, GM Church
    posted to protein-dna_interaction by medic0747 on 2007-04-10 13:28:06 as ** along with 2 people blobbybirdman yevishere
  • Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information.
    Bioinformatics, Vol. 20, No. 4. (1 March 2004), pp. 477-486.
    by S Ahmad, MM Gromiha, A Sarai
    posted to protein-dna_interaction by medic0747 on 2007-01-29 12:08:33 as **
  • A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
    Structure, Vol. 2, No. 4. (15 April 1994), pp. 317-326.
    by M Suzuki
    posted to protein-dna_interaction by medic0747 on 2007-03-21 14:26:47 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 electrostatic_potential protein-dna_interaction by medic0747 on 2007-09-26 12:35:08 as ** along with 2 people kaarsinogen carlescorbi
  • Do water molecules mediate protein-DNA recognition?
    J Mol Biol, Vol. 314, No. 3. (30 November 2001), pp. 619-632.
    by CK Reddy, A Das, B Jayaram
    posted to protein-dna_interaction water by medic0747 on 2007-04-13 14:14:51 as ** along with 2 people and 1 group yoonk sobolevnrm baker-group
  • Structural basis of DNA-protein recognition.
    Trends Biochem Sci, Vol. 14, No. 7. (July 1989), pp. 286-290.
    by RG Brennan, BW Matthews
    posted to protein-dna_interaction by medic0747 on 2007-03-21 14:30:13 as **
  • DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
    Proc Natl Acad Sci U S A, Vol. 91, No. 26. (20 December 1994), pp. 12357-12361.
    by M Suzuki, N Yagi
    posted to protein-dna_interaction by medic0747 on 2007-04-13 13:54:41 as **
  • The role of water in protein-DNA recognition.
    Annu Rev Biophys Biomol Struct, Vol. 33 (2004), pp. 343-361.
    by B Jayaram, T Jain
    posted to protein-dna_interaction by medic0747 on 2007-01-29 13:04:46 as ** along with 1 person yoonk
  • Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition.
    J Mol Biol, Vol. 313, No. 2. (19 October 2001), pp. 309-315.
    by JC Miller, CO Pabo
    posted to protein-dna_interaction by medic0747 on 2007-04-10 13:16:11 as **
  • Role of hydrogen bonds in protein-DNA recognition: effect of nonplanar amino groups.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 109, No. 20. (26 May 2005), pp. 10484-10492.
    by S Mukherjee, S Majumdar, D Bhattacharyya
    posted to protein-dna_interaction by medic0747 on 2007-04-13 16:34:21 as **
  • 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 protein-dna_interaction by medic0747 on 2007-04-12 19:14:23 as ** along with 1 person kaarsinogen
  • Common features in DNA recognition helices of eukaryotic transcription factors.
    EMBO J, Vol. 12, No. 8. (August 1993), pp. 3221-3226.
    by M Suzuki
    posted to protein-dna_interaction by medic0747 on 2007-04-13 13:56:18 as **
  • Protein and drug interactions in the minor groove of DNA.
    Nucleic Acids Res, Vol. 30, No. 5. (1 March 2002), pp. 1182-1191.
    by Z Morávek, S Neidle, B Schneider
    posted to drug protein-dna_interaction by medic0747 on 2007-04-13 15:31:32 as **
  • DNA recognition by proteins with the helix-turn-helix motif.
    Annu Rev Biochem, Vol. 59 (1990), pp. 933-969.
    by SC Harrison, AK Aggarwal
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:51:44 as **
  • Toward a Code for the Interactions of Zinc Fingers with DNA: Selection of Randomized Fingers Displayed on Phage
    PNAS, Vol. 91, No. 23. (8 November 1994), pp. 11163-11167.
    by Y Choo, A Klug
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:05:10 as ** along with 2 people aalibes perrywoo
  • 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_interaction by medic0747 on 2007-06-14 17:06:43 as ** along with 1 person aalibes
  • An overview of the structures of protein-DNA complexes.
    Genome Biol, Vol. 1, No. 1. (2000)
    by NM Luscombe, SE Austin, HM Berman, JM Thornton
    posted to protein-dna_interaction by medic0747 on 2007-03-20 14:43:06 as ** along with 3 people and 1 group kaarsinogen indigoviolet emptyhb EisenLab
  • Recognition of a DNA operator by the repressor of phage 434: a view at high resolution
    Science, Vol. 242, No. 4880. (11 November 1988), pp. 899-907.
    by Ak Aggarwal, Dw Rodgers, M Drottar, M Ptashne, Sc Harrison
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:17:54 as **
  • Conserved domains in DNA repair proteins and evolution of repair systems.
    Nucleic Acids Res, Vol. 27, No. 5. (1 March 1999), pp. 1223-1242.
    by L Aravind, DR Walker, EV Koonin
    posted to evolution protein-dna_interaction by medic0747 on 2007-09-26 14:58:35 as **
  • 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 protein-dna_interaction by medic0747 on 2007-04-10 13:05:45 as ** along with 2 people kaarsinogen roys
  • Cation-pi/H-bond stair motifs at protein-DNA interfaces.
    J Mol Biol, Vol. 319, No. 1. (24 May 2002), pp. 67-76.
    by M Rooman, J Liévin, E Buisine, R Wintjens
    posted to protein-dna_interaction by medic0747 on 2007-04-13 15:24:21 as **
  • Protein-DNA recognition.
    Annu Rev Biochem, Vol. 53 (1984), pp. 293-321.
    by CO Pabo, RT Sauer
    posted to protein-dna_interaction by medic0747 on 2007-03-21 14:16:14 as ** along with 1 person yoonk
  • Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.
    J Mol Biol, Vol. 345, No. 5. (4 February 2005), pp. 1027-1045.
    by TW Siggers, A Silkov, B Honig
    posted to protein-dna_interaction by medic0747 on 2007-06-14 15:56:29 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_interaction by medic0747 on 2007-01-29 11:54:59 as ** along with 2 people aalibes kaarsinogen
  • Homeodomain-DNA recognition.
    Cell, Vol. 78, No. 2. (29 July 1994), pp. 211-223.
    by WJ Gehring, YQ Qian, M Billeter, K Furukubo-Tokunaga, AF Schier, D Resendez-Perez, M Affolter, G Otting, K Wüthrich
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:45:23 as **
  • Co-crystal structure of TBP recognizing the minor groove of a TATA element.
    Nature, Vol. 365, No. 6446. (7 October 1993), pp. 520-527.
    by JL Kim, DB Nikolov, SK Burley
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:58:36 as **
  • Protein-DNA interaction. No code for recognition.
    Nature, Vol. 335, No. 6188. (22 September 1988), pp. 294-295.
    by BW Matthews
    posted to protein-dna_interaction by medic0747 on 2007-03-21 14:30:24 as **
  • Is there a code for protein-DNA recognition? Probab(ilistical)ly?
    BioEssays, Vol. 24, No. 5. (2002), pp. 466-475.
    by Panayiotis V Benos, Alan S Lapedes, Gary D Stormo
    posted to protein-dna_interaction by medic0747 on 2007-04-10 13:09:00 as **
  • Transcription factors: structural families and principles of DNA recognition.
    Annu Rev Biochem, Vol. 61 (1992), pp. 1053-1095.
    by CO Pabo, RT Sauer
    posted to protein-dna_interaction by medic0747 on 2007-03-21 14:24:27 as ** along with 3 people and 2 groups ana barry uz_labu_laimi structural_bioinformatics Bioinformatics
  • Refined 1.8 A crystal structure of the lambda repressor-operator complex.
    J Mol Biol, Vol. 227, No. 1. (5 September 1992), pp. 177-196.
    by LJ Beamer, CO Pabo
    posted to protein-dna_interaction by medic0747 on 2007-04-13 14:33:39 as **
  • DNA recognition code of transcription factors.
    Protein Eng, Vol. 8, No. 4. (April 1995), pp. 319-328.
    by M Suzuki, SE Brenner, M Gerstein, N Yagi
    posted to protein-dna_interaction by medic0747 on 2007-04-13 13:57:31 as **
  • Directional shape complementarity at the protein-DNA interface.
    J Mol Recognit, Vol. 16, No. 4. (g 2003), pp. 213-222.
    by CS Yeh, FM Chen, JY Wang, TL Cheng, MJ Hwang, WS Tzou
    posted to protein-dna_interaction by medic0747 on 2007-06-14 16:10:20 as **
  • A role for CH...O interactions in protein-DNA recognition.
    J Mol Biol, Vol. 277, No. 5. (17 April 1998), pp. 1129-1140.
    by Y Mandel-Gutfreund, H Margalit, RL Jernigan, VB Zhurkin
    posted to protein-dna_interaction by medic0747 on 2007-04-13 15:42:28 as **
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