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Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Nature communications, 2016-09, Vol.7 (1), p.12621-12621, Article 12621

2016

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Structure-based prediction of protein-nucleic acid binding using graph neural networks

Biophysical reviews, 2024-06, Vol.16 (3), p.297-314

2024

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Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site

Biochemistry (Easton), 2017-07, Vol.56 (29), p.3745-3753

2017

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Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

Cell, 2007-11, Vol.131 (3), p.530-543

2007

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Understanding Protein-DNA Recognition in the Context of Multi-Scale Genome Organization

Biophysical journal, 2020-02, Vol.118 (3), p.76a-76a

Rohs, Remo

2020

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Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

Nucleic acids research, 2013-09, Vol.41 (17), p.8368

2013

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Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding

Epigenetics & chromatin, 2018-02, Vol.11 (1), p.6-6, Article 6

2018

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Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection

Molecular biology and evolution, 2018-08, Vol.35 (8), p.1958-1967

2018

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Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation

PLoS genetics, 2016-07, Vol.12 (7), p.e1006120-e1006120

2016

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Correspondence: Reply to 'DNA shape is insufficient to explain binding'

Nature communications, 2017-06, Vol.8 (1), p.15644-15644, Article 15644

2017

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Correction: Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Nature communications, 2017-06, Vol.8 (1), p.1-1, Article 15723

2017

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A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA

ACS chemical biology, 2011-12, Vol.6 (12), p.1314-1320

2011

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Structural and Energetic Origins of Sequence-Specific DNA Bending: Monte Carlo Simulations of Papillomavirus E2-DNA Binding Sites

Structure (London), 2005-10, Vol.13 (10), p.1499-1509

2005

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Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling

Nucleic acids research, 2014-02, Vol.42 (4), p.2789

2014

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Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen

Cell reports (Cambridge), 2013-04, Vol.3 (4), p.1117-1127

2013

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Correction: Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Nature communications, 2016-11, Vol.7 (1), p.1-1, Article 13784

2016

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Physicochemical models of protein-DNA binding with standard and modified base pairs

Proceedings of the National Academy of Sciences - PNAS, 2023-01, Vol.120 (4), p.e2205796120-e2205796120

2023

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Absence of a simple code: how transcription factors read the genome

Trends in biochemical sciences (Amsterdam. Regular ed.), 2014-09, Vol.39 (9), p.381-399

2014

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Structure-Based Drug Design with a Deep Hierarchical Generative Model

Journal of chemical information and modeling, 2024-08, Vol.64 (16), p.6450-6463

2024

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DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding

Bioinformatics (Oxford, England), 2017-10, Vol.33 (19), p.3003-3010

2017

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Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding

Biophysical journal, 2024-01, Vol.123 (2), p.248-259

2024

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It is in the flanks: Conformational flexibility of transcription factor binding sites

Biophysical journal, 2022-10, Vol.121 (20), p.3765-3767

2022

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Biophysics: Flipping Watson and Crick

Nature (London), 2011-02, Vol.470 (7335), p.472-473

2011

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Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Nature structural & molecular biology, 2010-04, Vol.17 (4), p.423

2010

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Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding

Nucleic acids research, 2017-12, Vol.45 (21), p.12565

2017

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Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Structure-based prediction of protein-nucleic acid binding using graph neural networks

Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site

Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

Understanding Protein-DNA Recognition in the Context of Multi-Scale Genome Organization

Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding

Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection

Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation

Correspondence: Reply to 'DNA shape is insufficient to explain binding'

Correction: Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA

Structural and Energetic Origins of Sequence-Specific DNA Bending: Monte Carlo Simulations of Papillomavirus E2-DNA Binding Sites

Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling

Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen

Correction: Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Physicochemical models of protein-DNA binding with standard and modified base pairs

Absence of a simple code: how transcription factors read the genome

Structure-Based Drug Design with a Deep Hierarchical Generative Model

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding

Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding

It is in the flanks: Conformational flexibility of transcription factor binding sites

Biophysics: Flipping Watson and Crick

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding

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