ArticleNucleic acids research2010
DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation.The journal of physical chemistry. B · 2024Article
- Article
- Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease.Proteins · 2021Article
- DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method.International journal of molecular sciences · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.PLoS computational biology · 2020Article
- Investigating the Deoxyribonuclease Activity of CRM197 with Site-Directed Mutagenesis.ACS omega · 2019Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum.Journal of molecular modeling · 2019Article
- PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine.BMC bioinformatics · 2018Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context.Scientific reports · 2016Article
- Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes.BioMed research international · 2016Article
- Computational learning on specificity-determining residue-nucleotide interactions.Nucleic acids research · 2015Article
- A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.PLoS computational biology · 2015Article
- Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score.Nucleic acids research · 2015Article
- An overview of the prediction of protein DNA-binding sites.International journal of molecular sciences · 2015Review
- Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.PloS one · 2014Article
- DBSI: DNA-binding site identifier.Nucleic acids research · 2013Article
- PiDNA: Predicting protein-DNA interactions with structural models.Nucleic acids research · 2013Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNABINDPROT is designed to predict DNA-binding residues, based on the fluctuations of residues in high-frequency modes by the Gaussian network model. The residue pairs that display high mean-square distance fluctuations are analyzed with respect to DNA binding, which are then filtered with their evolutionary conservation profiles and ranked according to their DNA-binding propensities. If the analyses are based on the exact outcome of fluctuations in the highest mode, using a conservation threshold of 5, the results have a sensitivity, specificity, precision and accuracy of 9.3%, 90.5%, 18.1% and 78.6%, respectively, on a dataset of 36 unbound-bound protein structure pairs. These values increase up to 24.3%, 93.4%, 45.3% and 83.3% for the respective cases, when the neighboring two residues are considered. The relatively low sensitivity appears with the identified residues being selective and susceptible more for the binding core residues rather than all DNA-binding residues. The predicted residues that are not tagged as DNA-binding residues are those whose fluctuations are coupled with DNA-binding sites. They are in close proximity as well as plausible for other functional residues, such as ligand and protein-protein interaction sites. DNABINDPROT is free and open to all users without login requirement available at: http://www.prc.boun.edu.tr/appserv/prc/dnabindprot/.
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