ReviewCurrent opinion in structural biology2012
Atomistic modeling of protein-DNA interaction specificity: progress and applications.
Review in Current opinion in structural biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Caveat emptor: predicting and modeling protein-DNA recognition and binding via machine-learning computational approaches.Nucleic acids research · 2026Review
- Article
- Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations.Nucleic acids research · 2023Article
- Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites.Nucleic acids research · 2020Article
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- An efficient algorithm for improving structure-based prediction of transcription factor binding sites.BMC bioinformatics · 2017Article
- Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.Scientific reports · 2017Article
- Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes.The journal of physical chemistry. B · 2017Article
- Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing.Methods (San Diego, Calif.) · 2017Article
- Structure-based prediction of transcription factor binding specificity using an integrative energy function.Bioinformatics (Oxford, England) · 2016Article
- Knowledge-based three-body potential for transcription factor binding site prediction.IET systems biology · 2016Article
- An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.BMC bioinformatics · 2015Article
- Specificity and nonspecificity in RNA-protein interactions.Nature reviews. Molecular cell biology · 2015Review
- Quantitative modeling of transcription factor binding specificities using DNA shape.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.Nucleic acids research · 2014Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
- Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation.Molecular cell · 2014Article
- Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.PloS one · 2014Article
- Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model.Proteins · 2013Article
- Solvated protein-DNA docking using HADDOCK.Journal of biomolecular NMR · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
An accurate, predictive understanding of protein-DNA binding specificity is crucial for the successful design and engineering of novel protein-DNA binding complexes. In this review, we summarize recent studies that use atomistic representations of interfaces to predict protein-DNA binding specificity computationally. Although methods with limited structural flexibility have proven successful at recapitulating consensus binding sequences from wild-type complex structures, conformational flexibility is likely important for design and template-based modeling, where non-native conformations need to be sampled and accurately scored. A successful application of such computational modeling techniques in the construction of the TAL-DNA complex structure is discussed. With continued improvements in energy functions, solvation models, and conformational sampling, we are optimistic that reliable and large-scale protein-DNA binding prediction and engineering is a goal within reach.
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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.