Connecting protein structure with predictions of regulatory sites
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Summary
The utility of enlarging current structural genomics projects that exhaustively sample fold structure space to include all factors with significantly different DNA-binding specificities is highlighted, including higher eukaryotes.
- Type
- article
- Published
- 2007-04-24
- Cited by
- 69
- References
- 69
- Access
- Open access
- OpenAlex
- https://openalex.org/W17438293
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:9463975
Keywords
Coal basin, Coal, Process (computing), Environmental science, Underground coal gasification
References
- Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions
- Structural basis of Hox specificity
- Yersinia perturbs host cell signaling
- An improved map of conserved regulatory sites for Saccharomyces cerevisiae
- Structure of a HAP1–DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein
- The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions
- Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain
- Structure of a DNA-bound Ultrabithorax–Extradenticle homeodomain complex
- Structural basis for the diversity of DNA recognition by bZIP transcription factors
- Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
- Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.
- PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
- Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.
- Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
- SURVEY AND SUMMARY: Saccharomyces cerevisiae basic helix-loop-helix proteins regulate diverse biological processes.
- High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA.
- Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution.
- Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA
- Probabilistic code for DNA recognition by proteins of the EGR family.
- Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics.
Cited by
- DNA sequence motif: a jack of all trades for ChIP-Seq data.
- Détermination de la structure de protéines à l’aide de données faiblement résolues
- A computational method to search for DNA structural motifs in functional genomic elements.
- Structural Determinants of DNA-binding Specificity for Hox Proteins
- GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution
- Improving prediction fidelity of cellular metabolism with kinetic descriptions.
- Extrinsic and intrinsic nucleosome positioning signals
- Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism
- Towards a theoretical understanding of false positives in DNA motif finding
- Discovering multiple realistic TFBS motifs based on a generalized model
- Inference of Expanded Lrp-Like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction
- Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast
- Prediction of TF target sites based on atomistic models of protein-DNA complexes
- DBD2BS: connecting a DNA-binding protein with its binding sites
- Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures
- Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View
- Direct inference of protein–DNA interactions using compressed sensing methods
- Nuance in the double-helix and its role in protein-DNA recognition.
- The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks
- Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae
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