ArticleDatabase : the journal of biological databases and curation2021
Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces.
Article in Database : the journal of biological databases and curation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 14 citations in OpenAlex.
- DeepPNI: a language- and graph-based model for mutation-driven protein-nucleic acid binding energetics.Nucleic acids research · 2026Article
- Precise prediction of hotspot residues in protein-RNA complexes using graph attention networks and pretrained protein language models.Bioinformatics (Oxford, England) · 2025Article
- Decoding the effects of mutation on protein interactions using machine learning.Biophysics reviews · 2025Review
- Structural and functional prediction, evaluation, and validation in the post-sequencing era.Computational and structural biotechnology journal · 2024Review
- PNBACE: an ensemble algorithm to predict the effects of mutations on protein-nucleic acid binding affinity.BMC biology · 2024Article
- Prediction of Protein-DNA Interface Hot Spots Based on Empirical Mode Decomposition and Machine Learning.Genes · 2024Article
- Prediction of hot spots in protein-DNA binding interfaces based on discrete wavelet transform and wavelet packet transform.BMC bioinformatics · 2023Article
- VariBench, new variation benchmark categories and data sets.Frontiers in bioinformatics · 2023Article
- Research on the Computational Prediction of Essential Genes.Frontiers in cell and developmental biology · 2021Review
- Genomic Variation Prediction: A Summary From Different Views.Frontiers in cell and developmental biology · 2021Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-nucleic acid complexes play essential roles in regulating transcription, translation, DNA replication, repair and recombination, RNA processing and translocation. Site-directed mutagenesis has been extremely useful in understanding the principles of protein-DNA and protein-RNA interactions, and experimentally determined mutagenesis data are prerequisites for designing effective algorithms for predicting the binding affinity change upon mutation. However, a vital challenge in this area is the lack of sufficient public experimentally recognized mutation data, which leads to difficulties in developing computational prediction methods. In this article, we present Nabe, an integrated database of amino acid mutations and their effects on the binding free energy in protein-DNA and protein-RNA interactions for which binding affinities have been experimentally determined. Compared with existing databases and data sets, Nabe is the largest protein-nucleic acid mutation database, containing 2506 mutations in 473 protein-DNA and protein-RNA complexes, and of that 1751 are alanine mutations in 405 protein-nucleic acid complexes. For researchers to conveniently utilize the data, Nabe assembles protein-DNA and protein-RNA benchmark databases by adopting the data-processing procedures in the majority of models. To further facilitate users to query data, Nabe provides a searchable and graphical web page. Database URL: http://nabe.denglab.org.
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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.