212 related articles for article (PubMed ID: 29165643)
1. 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]
2. 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]
3. Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.
Andrabi M; Hutchins AP; Miranda-Saavedra D; Kono H; Nussinov R; Mizuguchi K; Ahmad S
Sci Rep; 2017 Jun; 7(1):4071. PubMed ID: 28642456
[TBL] [Abstract][Full Text] [Related]
4. 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]
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. Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles.
Kuznetsov VA
Methods Mol Biol; 2017; 1613():193-276. PubMed ID: 28849563
[TBL] [Abstract][Full Text] [Related]
7. Base-resolution methylation patterns accurately predict transcription factor bindings in vivo.
Xu T; Li B; Zhao M; Szulwach KE; Street RC; Lin L; Yao B; Zhang F; Jin P; Wu H; Qin ZS
Nucleic Acids Res; 2015 Mar; 43(5):2757-66. PubMed ID: 25722376
[TBL] [Abstract][Full Text] [Related]
8. Prediction of TF target sites based on atomistic models of protein-DNA complexes.
Angarica VE; Pérez AG; Vasconcelos AT; Collado-Vides J; Contreras-Moreira B
BMC Bioinformatics; 2008 Oct; 9():436. PubMed ID: 18922190
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.
Korolev N; Lyubartsev AP; Nordenskiöld L; Laaksonen A
J Mol Biol; 2001 May; 308(5):907-17. PubMed ID: 11352581
[TBL] [Abstract][Full Text] [Related]
11. A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Yang J; Ramsey SA
Bioinformatics; 2015 Nov; 31(21):3445-50. PubMed ID: 26130577
[TBL] [Abstract][Full Text] [Related]
12. Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.
Bauer AL; Hlavacek WS; Unkefer PJ; Mu F
PLoS Comput Biol; 2010 Nov; 6(11):e1001007. PubMed ID: 21124945
[TBL] [Abstract][Full Text] [Related]
13. DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.
Mathelier A; Xin B; Chiu TP; Yang L; Rohs R; Wasserman WW
Cell Syst; 2016 Sep; 3(3):278-286.e4. PubMed ID: 27546793
[TBL] [Abstract][Full Text] [Related]
14. Using DNA duplex stability information for transcription factor binding site discovery.
Gordân R; Hartemink AJ
Pac Symp Biocomput; 2008; ():453-64. PubMed ID: 18229707
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. 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]
17. Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data.
Tan C; Takada S
J Chem Theory Comput; 2018 Jul; 14(7):3877-3889. PubMed ID: 29806939
[TBL] [Abstract][Full Text] [Related]
18. An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization.
Qian Z; Lu L; Liu X; Cai YD; Li Y
Bioinformatics; 2007 Sep; 23(18):2449-54. PubMed ID: 17623704
[TBL] [Abstract][Full Text] [Related]
19. Structure-based ab initio prediction of transcription factor-binding sites.
Liu LA; Bader JS
Methods Mol Biol; 2009; 541():23-41. PubMed ID: 19381536
[TBL] [Abstract][Full Text] [Related]
20. An in-the-groove view of DNA structures in complexes with proteins.
Suzuki M; Yagi N
J Mol Biol; 1996 Feb; 255(5):677-87. PubMed ID: 8636970
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]