216 related articles for article (PubMed ID: 35978548)
1. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.
Ghoshdastidar D; Bansal M
Biophys J; 2022 Oct; 121(20):3987-4000. PubMed ID: 35978548
[TBL] [Abstract][Full Text] [Related]
2. Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.
Yella VR; Bhimsaria D; Ghoshdastidar D; Rodríguez-Martínez JA; Ansari AZ; Bansal M
Nucleic Acids Res; 2018 Dec; 46(22):11883-11897. PubMed ID: 30395339
[TBL] [Abstract][Full Text] [Related]
3. Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.
Jiang Y; Chiu TP; Mitra R; Rohs R
Biophys J; 2024 Jan; 123(2):248-259. PubMed ID: 38130056
[TBL] [Abstract][Full Text] [Related]
4. A widespread role of the motif environment in transcription factor binding across diverse protein families.
Dror I; Golan T; Levy C; Rohs R; Mandel-Gutfreund Y
Genome Res; 2015 Sep; 25(9):1268-80. PubMed ID: 26160164
[TBL] [Abstract][Full Text] [Related]
5. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.
Oliver P; Peralta-Gil M; Tabche ML; Merino E
BMC Genomics; 2016 Aug; 17(1):686. PubMed ID: 27567672
[TBL] [Abstract][Full Text] [Related]
6. Enhancers display constrained sequence flexibility and context-specific modulation of motif function.
Reiter F; de Almeida BP; Stark A
Genome Res; 2023 Mar; 33(3):346-358. PubMed ID: 36941077
[TBL] [Abstract][Full Text] [Related]
7. Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation.
Patra P; Gao YQ
J Phys Chem B; 2022 Nov; 126(45):9187-9206. PubMed ID: 36322688
[TBL] [Abstract][Full Text] [Related]
8. A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.
He X; Chen CC; Hong F; Fang F; Sinha S; Ng HH; Zhong S
PLoS One; 2009 Dec; 4(12):e8155. PubMed ID: 19956545
[TBL] [Abstract][Full Text] [Related]
9. A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.
Nikolova EN; Stanfield RL; Dyson HJ; Wright PE
Biochemistry; 2020 May; 59(20):1909-1926. PubMed ID: 32352758
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.
Martin V; Zhuang F; Zhang Y; Pinheiro K; Gordân R
Nucleic Acids Res; 2023 Nov; 51(21):11600-11612. PubMed ID: 37889068
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors.
Hörberg J; Moreau K; Tamás MJ; Reymer A
Nucleic Acids Res; 2021 Sep; 49(16):9280-9293. PubMed ID: 34387667
[TBL] [Abstract][Full Text] [Related]
14. Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
Afek A; Cohen H; Barber-Zucker S; Gordân R; Lukatsky DB
PLoS Comput Biol; 2015 Aug; 11(8):e1004429. PubMed ID: 26285121
[TBL] [Abstract][Full Text] [Related]
15. Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context.
Rudnizky S; Khamis H; Malik O; Squires AH; Meller A; Melamed P; Kaplan A
Nucleic Acids Res; 2018 Feb; 46(3):1513-1524. PubMed ID: 29253225
[TBL] [Abstract][Full Text] [Related]
16. Characterization of sequence determinants of enhancer function using natural genetic variation.
Yang MG; Ling E; Cowley CJ; Greenberg ME; Vierbuchen T
Elife; 2022 Aug; 11():. PubMed ID: 36043696
[TBL] [Abstract][Full Text] [Related]
17. Unraveling determinants of transcription factor binding outside the core binding site.
Levo M; Zalckvar E; Sharon E; Dantas Machado AC; Kalma Y; Lotam-Pompan M; Weinberger A; Yakhini Z; Rohs R; Segal E
Genome Res; 2015 Jul; 25(7):1018-29. PubMed ID: 25762553
[TBL] [Abstract][Full Text] [Related]
18. DNA structural properties of DNA binding sites for 21 transcription factors in the mycobacterial genome.
Dey U; Olymon K; Banik A; Abbas E; Yella VR; Kumar A
Front Cell Infect Microbiol; 2023; 13():1147544. PubMed ID: 37396305
[No Abstract] [Full Text] [Related]
19. DNase footprint signatures are dictated by factor dynamics and DNA sequence.
Sung MH; Guertin MJ; Baek S; Hager GL
Mol Cell; 2014 Oct; 56(2):275-285. PubMed ID: 25242143
[TBL] [Abstract][Full Text] [Related]
20. Sequence features of DNA binding sites reveal structural class of associated transcription factor.
Narlikar L; Hartemink AJ
Bioinformatics; 2006 Jan; 22(2):157-63. PubMed ID: 16267080
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
