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medic0747s library [179 articles]

Neue Artikel in medic0747s Bibliothek.
  • 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 **
  • 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 **
  • 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
  • Structure Based Prediction of Binding Residues on DNA-binding Proteins.
    Conf Proc IEEE Eng Med Biol Soc, Vol. 3 (2005), pp. 2611-2614.
    by N Bhardwaj, R Langlois, G Zhao, H Lu
    posted to protein-dna_interaction by medic0747 on 2007-09-26 12:36:49 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
  • Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies
    BMC Structural Biology, Vol. 7 (17 May 2007), 31.
    by Ozlem Keskin
    posted to protein_flexibility by medic0747 on 2007-06-26 15:26:45 as ** along with 1 person choonpeng
  • Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.
    Biopolymers, Vol. 78, No. 6. (15 August 2005), pp. 318-328.
    by HP Shanahan, JM Thornton
    posted to protein_surface by medic0747 on 2007-06-17 12:13:10 as ** along with 1 person and 1 group cat_worth structural_bioinformatics
  • Classification of Protein-DNA Complexes Based on Structural Descriptors
    Structure, Vol. 14, No. 9. (September 2006), pp. 1355-1367.
    by Ponraj Prabakaran, Jorg G Siebers, Shandar Ahmad, Michael M Gromiha, Maria G Singarayan, Akinori Sarai
    posted to protein-dna_interaction by medic0747 on 2007-06-14 17:10:12 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_interaction by medic0747 on 2007-06-14 17:06:43 as **
  • 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 1 person aalibes
  • 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 **
  • 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 **
  • 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 **
  • 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
  • Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
    BMC Struct Biol, Vol. 5 (16 August 2005)
    by S De, O Krishnadev, N Srinivasan, N Rekha
    posted to protein-protein_interaction by medic0747 on 2007-05-11 15:35:27 as ** along with 2 people bicko choonpeng
  • The packing density in proteins: standard radii and volumes.
    J Mol Biol, Vol. 290, No. 1. (2 July 1999), pp. 253-266.
    by J Tsai, R Taylor, C Chothia, M Gerstein
    posted to protein vdw by medic0747 on 2007-05-11 13:31:15 as ** along with 5 people and 3 groups sobolevnrm ana barry bicko blackbart baker-group structural_bioinformatics Bioinformatics
  • Hydrophobicity of amino acid residues in globular proteins
    Science, Vol. 229, No. 4716. (30 August 1985), pp. 834-838.
    by Gd Rose, Ar Geselowitz, Gj Lesser, Rh Lee, Mh Zehfus
    posted to hydrophobicity protein by medic0747 on 2007-05-11 12:45:26 as ** along with 1 person ashaytan
  • A simple method for displaying the hydropathic character of a protein.
    J Mol Biol, Vol. 157, No. 1. (5 May 1982), pp. 105-132.
    by J Kyte, RF Doolittle
    posted to protein by medic0747 on 2007-05-11 12:39:04 as ** along with 5 people thaliana chad_davis dgront netterpaladin ashaytan
  • Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.
    Biophys J, Vol. 92, No. 3. (1 February 2007), pp. 769-786.
    by CM Topham, JC Smith
    posted to protein-na_interaction by medic0747 on 2007-04-13 16:47:09 as **
  • 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 **
  • 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 **
  • Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns.
    FEBS Lett, Vol. 552, No. 2-3. (25 September 2003), pp. 231-239.
    by H Kim, E Jeong, SW Lee, K Han
    posted to protein-rna_interaction by medic0747 on 2007-04-13 16:21:46 as **
  • 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 protein-dna_interaction by medic0747 on 2007-04-13 16:20:30 as ** along with 1 person kaarsinogen
  • 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 **
  • 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 **
  • Structure-based analysis of protein-RNA interactions using the program ENTANGLE.
    J Mol Biol, Vol. 311, No. 1. (3 August 2001), pp. 75-86.
    by J Allers, Y Shamoo
    posted to protein-rna_interaction by medic0747 on 2007-04-13 15:33:42 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 **
  • Contribution of cation-pi interactions to the stability of protein-DNA complexes.
    J Mol Biol, Vol. 302, No. 2. (15 September 2000), pp. 395-410.
    by R Wintjens, J Liévin, M Rooman, E Buisine
    posted to protein-dna_interaction by medic0747 on 2007-04-13 15:27:19 as **
  • 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 **
  • Statistical analysis of atomic contacts at RNA-protein interfaces.
    J Mol Recognit, Vol. 14, No. 4. (g 2001), pp. 199-214.
    by M Treger, E Westhof
    posted to protein-rna_interaction by medic0747 on 2007-04-13 15:14:46 as ** along with 1 person lillekatt
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 1 person and 1 group sobolevnrm baker-group
  • 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
  • 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
  • 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 **
  • 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 **
  • 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 **
  • 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
  • Bifurcated hydrogen bonds and flip[mdash]flop conformation in a modified nucleic acid base, gc6Ade
    Nature, Vol. 260, No. 5554. (29 April 1976), pp. 807-808.
    by R Parthasarathy, Manuel Soriano-Garcia, Girish B Chheda
    posted to hydrogen_bond by medic0747 on 2007-04-12 10:38:39 as **
  • Geometric criteria of hydrogen bonds in proteins and identification of "bifurcated" hydrogen bonds.
    Protein Eng, Vol. 15, No. 5. (May 2002), pp. 359-363.
    by IY Torshin, IT Weber, RW Harrison
    posted to hydrogen_bond by medic0747 on 2007-04-12 10:36:45 as ** along with 2 people and 3 groups barry sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys.
    Nucleic Acids Res, Vol. 32, No. 17. (2004), pp. 5147-5162.
    by Y Chen, T Kortemme, T Robertson, D Baker, G Varani
    posted to protein-rna_interaction by medic0747 on 2007-04-10 13:32:48 as ** along with 1 person jwm
  • 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
  • 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 2 people emptyhb yevishere
  • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.
    Nucleic Acids Res, Vol. 30, No. 5. (1 March 2002), pp. 1255-1261.
    by ML Bulyk, PL Johnson, GM Church
    posted to protein-dna_interaction by medic0747 on 2007-04-10 13:19:43 as ** along with 1 person yevishere
  • 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 **
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