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Quantum annealing versus classical machine learning applied to a simplified computational biology problem.
- Published in:
- NPJ Quantum Information, 2018, v. 4, n. 1, p. N.PAG, doi. 10.1038/s41534-018-0060-8
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- Article
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.
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- Nucleic Acids Research, 2018, v. 46, n. 5, p. 2636, doi. 10.1093/nar/gky033
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- Article
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.
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- Nucleic Acids Research, 2017, v. 45, n. 22, p. 12877, doi. 10.1093/nar/gkx1145
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- Article
Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding.
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- Nucleic Acids Research, 2017, v. 45, n. 21, p. 12565, doi. 10.1093/nar/gkx915
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- Article
DNAproDB: an interactive tool for structural analysis of DNA--protein complexes.
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- Nucleic Acids Research, 2017, v. 45, n. W1, p. W89, doi. 10.1093/nar/gkx272
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- Article
Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED.
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- Nucleic Acids Research, 2015, v. 43, n. 4, p. 2199, doi. 10.1093/nar/gku1377
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- Article
GBshape: a genome browser database for DNA shape annotations.
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- Nucleic Acids Research, 2015, v. 43, n. D1, p. D103, doi. 10.1093/nar/gku977
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- Article
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.
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- Nucleic Acids Research, 2014, v. 42, n. 4, p. 2789, doi. 10.1093/nar/gkt1219
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- Article
TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
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- Nucleic Acids Research, 2014, v. 42, n. D1, p. D148, doi. 10.1093/nar/gkt1087
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- Article
Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein–DNA interactions.
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- Nucleic Acids Research, 2013, v. 41, n. 18, p. 8748, doi. 10.1093/nar/gkt630
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- Article
Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
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- Nucleic Acids Research, 2013, v. 41, n. 17, p. 1, doi. 10.1093/nar/gkt862
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- Article
Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion.
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- Nucleic Acids Research, 2013, v. 41, n. 17, p. 8368, doi. 10.1093/nar/gkt584
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- Article
Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.
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- Nucleic Acids Research, 2013, v. 41, n. 13, p. 6750, doi. 10.1093/nar/gkt357
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- Publication type:
- Article
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.
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- Nucleic Acids Research, 2013, v. 41, p. W56, doi. 10.1093/nar/gkt437
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- Article
Genome information processing by the INO80 chromatin remodeler positions nucleosomes.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23016-z
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- Article
Exposing the secrets of sex determination.
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- Nature Structural & Molecular Biology, 2015, v. 22, n. 6, p. 437, doi. 10.1038/nsmb.3042
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- Article
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs.
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- Nature Structural & Molecular Biology, 2010, v. 17, n. 4, p. 423, doi. 10.1038/nsmb.1800
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- Article
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics.
- Published in:
- Bioinformatics, 2022, v. 38, n. 22, p. 5121, doi. 10.1093/bioinformatics/btac653
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- Article
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.
- Published in:
- Scientific Reports, 2015, p. 8733, doi. 10.1038/ncomms9733
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- Article
Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection.
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- Molecular Biology & Evolution, 2018, v. 35, n. 8, p. 1958, doi. 10.1093/molbev/msy099
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- Article
Biophysics: Flipping Watson and Crick.
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- Nature, 2011, v. 470, n. 7335, p. 472, doi. 10.1038/470472a
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- Article
The role of DNA shape in protein–DNA recognition.
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- Nature, 2009, v. 461, n. 7268, p. 1248, doi. 10.1038/nature08473
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- Article
Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations.
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- Nucleic Acids Research, 2005, v. 33, n. 22, p. 7048, doi. 10.1093/nar/gki1008
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- Article
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.
- Published in:
- Molecular Systems Biology, 2017, v. 13, n. 2, p. n/a, doi. 10.15252/msb.20167238
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- Article
Correspondence: Reply to 'DNA shape is insufficient to explain binding'.
- Published in:
- Nature Communications, 2017, v. 8, n. 6, p. 15644, doi. 10.1038/ncomms15644
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- Article
Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.
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- Nature Communications, 2017, v. 8, n. 6, p. 15723, doi. 10.1038/ncomms15723
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- Article
Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.
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- Nature Communications, 2016, v. 7, n. 11, p. 13784, doi. 10.1038/ncomms13784
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- Article
Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.
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- Nature Communications, 2016, v. 7, n. 9, p. 12621, doi. 10.1038/ncomms12621
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- Publication type:
- Article
Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.
- Published in:
- Nature Communications, 2015, v. 6, n. 12, p. 10264, doi. 10.1038/ncomms10264
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- Publication type:
- Article
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.
- Published in:
- Nature Communications, 2015, v. 6, n. 10, p. 8733, doi. 10.1038/ncomms9733
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- Publication type:
- Article
Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.
- Published in:
- Nature Communications, 2015, v. 6, n. 7, p. 7642, doi. 10.1038/ncomms8642
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- Article
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum.
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- Nucleic Acids Research, 2024, v. 52, n. 17, p. 10161, doi. 10.1093/nar/gkae585
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- Article
Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.
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- Nucleic Acids Research, 2024, v. 52, n. W1, p. W7, doi. 10.1093/nar/gkae433
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- Article
RNAscape: geometric mapping and customizable visualization of RNA structure.
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- Nucleic Acids Research, 2024, v. 52, n. W1, p. W354, doi. 10.1093/nar/gkae269
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- Article
DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.
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- Nucleic Acids Research, 2023, v. 51, n. 11, p. 5621, doi. 10.1093/nar/gkad372
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- Article
Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.
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- Nucleic Acids Research, 2020, v. 48, n. 15, p. 8529, doi. 10.1093/nar/gkaa642
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- Article
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.
- Published in:
- Nucleic Acids Research, 2020, v. 48, n. D1, p. D246, doi. 10.1093/nar/gkz970
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- Publication type:
- Article
DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes.
- Published in:
- Nucleic Acids Research, 2020, v. 48, n. D1, p. D277, doi. 10.1093/nar/gkz889
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- Article
Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians.
- Published in:
- Journal of Computational Chemistry, 2006, v. 27, n. 3, p. 309, doi. 10.1002/jcc.20345
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- Article
Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes.
- Published in:
- Biochemistry & Molecular Biology Education, 2012, v. 40, n. 6, p. 400, doi. 10.1002/bmb.20650
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- Article
How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.
- Published in:
- BioEssays, 2016, v. 38, n. 7, p. 605, doi. 10.1002/bies.201600005
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- Article
Evolving insights on how cytosine methylation affects protein-DNA binding.
- Published in:
- Briefings in Functional Genomics, 2015, v. 14, n. 1, p. 61, doi. 10.1093/bfgp/elu040
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- Article
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding.
- Published in:
- Epigenetics & Chromatin, 2018, v. 11, p. 1, doi. 10.1186/s13072-018-0174-4
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- Article
DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.
- Published in:
- Bioinformatics, 2017, v. 33, n. 19, p. 3003, doi. 10.1093/bioinformatics/btx336
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- Article
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
- Published in:
- Bioinformatics, 2016, v. 32, n. 8, p. 1211, doi. 10.1093/bioinformatics/btv735
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- Article
Humanizing the yeast origin recognition complex.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-020-20277-y
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- Publication type:
- Article
Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation.
- Published in:
- PLoS Genetics, 2016, v. 12, n. 7, p. 1, doi. 10.1371/journal.pgen.1006120
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- Article