BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

251 related articles for article (PubMed ID: 29040720)

  • 1. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.
    Chiu TP; Rao S; Mann RS; Honig B; Rohs R
    Nucleic Acids Res; 2017 Dec; 45(21):12565-12576. PubMed ID: 29040720
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.
    Hancock SP; Ghane T; Cascio D; Rohs R; Di Felice R; Johnson RC
    Nucleic Acids Res; 2013 Jul; 41(13):6750-60. PubMed ID: 23661683
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins.
    Kribelbauer JF; Loker RE; Feng S; Rastogi C; Abe N; Rube HT; Bussemaker HJ; Mann RS
    Mol Cell; 2020 Apr; 78(1):152-167.e11. PubMed ID: 32053778
    [TBL] [Abstract][Full Text] [Related]  

  • 4. The role of DNA shape in protein-DNA recognition.
    Rohs R; West SM; Sosinsky A; Liu P; Mann RS; Honig B
    Nature; 2009 Oct; 461(7268):1248-53. PubMed ID: 19865164
    [TBL] [Abstract][Full Text] [Related]  

  • 5. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.
    Bishop EP; Rohs R; Parker SC; West SM; Liu P; Mann RS; Honig B; Tullius TD
    ACS Chem Biol; 2011 Dec; 6(12):1314-20. PubMed ID: 21967305
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
    Dror I; Zhou T; Mandel-Gutfreund Y; Rohs R
    Nucleic Acids Res; 2014 Jan; 42(1):430-41. PubMed ID: 24078250
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.
    Li J; Sagendorf JM; Chiu TP; Pasi M; Perez A; Rohs R
    Nucleic Acids Res; 2017 Dec; 45(22):12877-12887. PubMed ID: 29165643
    [TBL] [Abstract][Full Text] [Related]  

  • 8. DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.
    Zhou T; Yang L; Lu Y; Dror I; Dantas Machado AC; Ghane T; Di Felice R; Rohs R
    Nucleic Acids Res; 2013 Jul; 41(Web Server issue):W56-62. PubMed ID: 23703209
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Interchange of DNA-binding modes in the deformed and ultrabithorax homeodomains: a structural role for the N-terminal arm.
    Frazee RW; Taylor JA; Tullius TD
    J Mol Biol; 2002 Nov; 323(4):665-83. PubMed ID: 12419257
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Binding regularities in complexes of transcription factors with operator DNA: homeodomain family.
    Chirgadze YN; Zheltukhin EI; Polozov RV; Sivozhelezov VS; Ivanov VV
    J Biomol Struct Dyn; 2009 Jun; 26(6):687-700. PubMed ID: 19385698
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Origins of specificity in protein-DNA recognition.
    Rohs R; Jin X; West SM; Joshi R; Honig B; Mann RS
    Annu Rev Biochem; 2010; 79():233-69. PubMed ID: 20334529
    [TBL] [Abstract][Full Text] [Related]  

  • 12. A DNA minor groove electronegative potential genome map based on photo-chemical probing.
    Lindemose S; Nielsen PE; Hansen M; Møllegaard NE
    Nucleic Acids Res; 2011 Aug; 39(14):6269-76. PubMed ID: 21478164
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.
    Azad RN; Zafiropoulos D; Ober D; Jiang Y; Chiu TP; Sagendorf JM; Rohs R; Tullius TD
    Nucleic Acids Res; 2018 Mar; 46(5):2636-2647. PubMed ID: 29390080
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Quantitative modeling of transcription factor binding specificities using DNA shape.
    Zhou T; Shen N; Yang L; Abe N; Horton J; Mann RS; Bussemaker HJ; Gordân R; Rohs R
    Proc Natl Acad Sci U S A; 2015 Apr; 112(15):4654-9. PubMed ID: 25775564
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.
    Yang L; Orenstein Y; Jolma A; Yin Y; Taipale J; Shamir R; Rohs R
    Mol Syst Biol; 2017 Feb; 13(2):910. PubMed ID: 28167566
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Minor groove deformability of DNA: a molecular dynamics free energy simulation study.
    Zacharias M
    Biophys J; 2006 Aug; 91(3):882-91. PubMed ID: 16698780
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies.
    Hamelberg D; Williams LD; Wilson WD
    Nucleic Acids Res; 2002 Aug; 30(16):3615-23. PubMed ID: 12177304
    [TBL] [Abstract][Full Text] [Related]  

  • 18. A unified approach for quantifying and interpreting DNA shape readout by transcription factors.
    Rube HT; Rastogi C; Kribelbauer JF; Bussemaker HJ
    Mol Syst Biol; 2018 Feb; 14(2):e7902. PubMed ID: 29472273
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Structures of an all-α protein running along the DNA major groove.
    Yu LY; Cheng W; Zhou K; Li WF; Yu HM; Gao X; Shen X; Wu Q; Chen Y; Zhou CZ
    Nucleic Acids Res; 2016 May; 44(8):3936-45. PubMed ID: 26939889
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site.
    Shao Y; Feldman-Cohen LS; Osuna R
    J Mol Biol; 2008 Jul; 380(2):327-39. PubMed ID: 18514225
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 13.