ArticleBMC bioinformatics2014
DBBP: database of binding pairs in protein-nucleic acid interactions.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 19 citations in OpenAlex.
- rbpTransformer: A novel deep learning model for prediction of piRNA and mRNA bindings.PloS one · 2025Article
- Ned Seeman and the prediction of amino acid-basepair motifs mediating protein-nucleic acid recognition.Biophysical journal · 2022Review
- RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources.International journal of molecular sciences · 2022Article
- Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.PLoS computational biology · 2020Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Sequence-Based Prediction of RNA-Binding Residues in Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInteraction of proteins with other molecules plays an important role in many biological activities. As many structures of protein-DNA complexes and protein-RNA complexes have been determined in the past years, several databases have been constructed to provide structure data of the complexes. However, the information on the binding sites between proteins and nucleic acids is not readily available from the structure data since the data consists mostly of the three-dimensional coordinates of the atoms in the complexes.
resultsWe analyzed the huge amount of structure data for the hydrogen bonding interactions between proteins and nucleic acids and developed a database called DBBP (DataBase of Binding Pairs in protein-nucleic acid interactions, http://bclab.inha.ac.kr/dbbp). DBBP contains 44,955 hydrogen bonds (H-bonds) of protein-DNA interactions and 77,947 H-bonds of protein-RNA interactions.
conclusionsAnalysis of the huge amount of structure data of protein-nucleic acid complexes is labor-intensive, yet provides useful information for studying protein-nucleic acid interactions. DBBP provides the detailed information of hydrogen-bonding interactions between proteins and nucleic acids at various levels from the atomic level to the residue level. The binding information can be used as a valuable resource for developing a computational method aiming at predicting new binding sites in proteins or nucleic acids.
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