ArticleNucleic acids research2022
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 55 citations in OpenAlex.
- ProRB: a structure-free unified framework for joint prediction and design of protein-RNA interactions.Nucleic acids research · 2026Article
- TDP-43 controls RNA structure through high affinity lattice interactions.Nature communications · 2026Article
- DeepPNI: a language- and graph-based model for mutation-driven protein-nucleic acid binding energetics.Nucleic acids research · 2026Article
- M2-PRNet: multi-scale and multi-modal learning for protein-RNA binding affinity prediction.Bioinformatics (Oxford, England) · 2026Article
- Experimentally Tuned Protein-RNA Rosetta Score Function using Bayesian Optimization.bioRxiv : the preprint server for biology · 2026Article
- PANTHER Score: Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression.RNA (New York, N.Y.) · 2026Article
- Ribocentre-aptamer: an integrative, structure-focused database for RNA aptamers.Nucleic acids research · 2026Article
- Large-scale multi-omic biosequence transformers for modeling protein-nucleic acid interactions.PloS one · 2026Article
- RNApedia: a database of structural protein-RNA interactions.Frontiers in bioinformatics · 2026Article
- Topological machine learning for protein-nucleic acid binding affinity changes upon mutation.Machine learning: science and technology · 2025Article
- TDP-43 controls RNA structure through high affinity lattice interactions.bioRxiv : the preprint server for biology · 2025Article
- Article
- Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions.ArXiv · 2025Article
- RLSuccSite: succinylation sites prediction based on reinforcement learning dynamic with balanced reward mechanism and three-peaks enhanced method for physicochemical property scores.Journal of cheminformatics · 2025Article
- Decoding the effects of mutation on protein interactions using machine learning.Biophysics reviews · 2025Review
- Overview and limitations of database in global traditional medicines: A narrative review.Acta pharmacologica Sinica · 2025Review
- Article
- Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- 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
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation and packaging. The binding affinities of protein-DNA and protein-RNA complexes are important for elucidating the mechanism of protein-nucleic acid recognition. Although experimental data on binding affinity are reported abundantly in the literature, no well-curated database is currently available for protein-nucleic acid binding affinity. We have developed a database, ProNAB, which contains more than 20 000 experimental data for the binding affinities of protein-DNA and protein-RNA complexes. Each entry provides comprehensive information on sequence and structural features of a protein, nucleic acid and its complex, experimental conditions, thermodynamic parameters such as dissociation constant (Kd), binding free energy (ΔG) and change in binding free energy upon mutation (ΔΔG), and literature information. ProNAB is cross-linked with GenBank, UniProt, PDB, ProThermDB, PROSITE, DisProt and Pubmed. It provides a user-friendly web interface with options for search, display, sorting, visualization, download and upload the data. ProNAB is freely available at https://web.iitm.ac.in/bioinfo2/pronab/ and it has potential applications such as understanding the factors influencing the affinity, development of prediction tools, binding affinity change upon mutation and design complexes with the desired affinity.
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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.