ArticleBMC bioinformatics2010
The Protein-DNA Interface database.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.NPJ systems biology and applications · 2026Article
- Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.Briefings in bioinformatics · 2024Review
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- ProDFace: A web-tool for the dissection of protein-DNA interfaces.Frontiers in molecular biosciences · 2022Article
- pyDockDNA: A new web server for energy-based protein-DNA docking and scoring.Frontiers in molecular biosciences · 2022Article
- Protein embeddings and deep learning predict binding residues for various ligand classes.Scientific reports · 2021Article
- In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase fromPharmaceuticals (Basel, Switzerland) · 2021Article
- PredictProtein - Predicting Protein Structure and Function for 29 Years.Nucleic acids research · 2021Article
- DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2020Article
- Design of inhibitors of thymidylate kinase fromJournal of biomolecular structure & dynamics · 2019Article
- Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions.Bioinformatics (Oxford, England) · 2019Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures.Briefings in bioinformatics · 2019Article
- DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2017Article
- High-resolution biophysical analysis of the dynamics of nucleosome formation.Scientific reports · 2016Article
- PDIviz: analysis and visualization of protein-DNA binding interfaces.Bioinformatics (Oxford, England) · 2015Article
- An overview of the prediction of protein DNA-binding sites.International journal of molecular sciences · 2015Review
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
- DBBP: database of binding pairs in protein-nucleic acid interactions.BMC bioinformatics · 2014Article
- Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 A or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface.We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.
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