ArticleNucleic acids research2013
NPIDB: Nucleic acid-Protein Interaction DataBase.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- RNApedia: a database of structural protein-RNA interactions.Frontiers in bioinformatics · 2026Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- A role for pH dynamics regulating transcription factor DNA-binding selectivity.Nucleic acids research · 2025Article
- Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Bootstrap Model of Prebiotic Networks of Proteins and Nucleic Acids.Life (Basel, Switzerland) · 2022Article
- Protein-RNA interaction prediction with deep learning: structure matters.Briefings in bioinformatics · 2022Article
- A deep learning framework to predict binding preference of RNA constituents on protein surface.Nature communications · 2019Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction.Journal of computer-aided molecular design · 2018Article
- A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces.RSC advances · 2018Article
- Data of protein-RNA binding sites.Data in brief · 2017Article
- Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.Proteins · 2017Article
- Sequence-Based Prediction of RNA-Binding Residues in Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data.Frontiers in genetics · 2017Article
- Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis.Experimental & molecular medicine · 2016Article
- RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.BMC bioinformatics · 2016Article
- Structures of an all-α protein running along the DNA major groove.Nucleic acids research · 2016Article
- An updated version of NPIDB includes new classifications of DNA-protein complexes and their families.Nucleic acids research · 2016Article
- DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.Database : the journal of biological databases and curation · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.
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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.