ArticleProteome science2004
From sequence to structure and back again: approaches for predicting protein-DNA binding.
Article in Proteome science, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Article
- Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations.Journal of computer-aided molecular design · 2018Article
- Article
- Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties.Proteome science · 2011Article
- Direct inference of protein-DNA interactions using compressed sensing methods.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements.Genome research · 2009Article
- Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.BMC bioinformatics · 2007Article
- A new systematic computational approach to predicting target genes of transcription factors.Nucleic acids research · 2007Article
- Scoring functions for transcription factor binding site prediction.BMC bioinformatics · 2005Article
- Identification of the 'NORE' (N-Oct-3 responsive element), a novel structural motif and composite element.Nucleic acids research · 2005Article
- Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation.Nucleic acids research · 2005Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulation in higher organisms is achieved by a complex network of transcription factors (TFs). Modulating gene expression and exploring gene function are major aims in molecular biology. Furthermore, the identification of putative target genes for a certain TF serve as powerful tools for specific targeting of rational drugs.Detecting the short and variable transcription factor binding sites (TFBSs) in genomic DNA is an intriguing challenge for computational and structural biologists. Fast and reliable computational methods for predicting TFBSs on a whole-genome scale offer several advantages compared to the current experimental methods that are rather laborious and slow. Two main approaches are being explored, advanced sequence-based algorithms and structure-based methods.The aim of this review is to outline the computational and experimental methods currently being applied in the field of protein-DNA interactions. With a focus on the former, the current state of the art in modeling these interactions is discussed. Surveying sequence and structure-based methods for predicting TFBSs, we conclude that in order to achieve a sound and specific method applicable on genomic sequences it is desirable and important to bring these two approaches together.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.