ArticleNucleic acids research2015
High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 1 of them a synthesis that pooled it.
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Who cites it
95 citing papers in PubMed, 1 synthesis or guideline pooled it, 171 citations in OpenAlex.
- Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction.Genes · 2024Pooled it
- AnThe Journal of general virology · 2026Article
- DNAreader: accurate prediction of DNA-binding residues in structured and disordered proteins using transformers and contrastive learning.Nucleic acids research · 2026Article
- Article
- Predicting molecular recognition features in protein sequences with MoRFchibi 2.0.BMC bioinformatics · 2026Article
- CB-Search: a method for searching for similar protein motifs with biased compositions.BMC bioinformatics · 2026Article
- LUCID: An Integrative Approach for Target Discovery and dsRNA Design in Plant Fungal Pathogens.Plant biotechnology journal · 2026Article
- Hybrid deep learning with protein language models and dual-path architecture for predicting IDP functions.Briefings in bioinformatics · 2026Article
- Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases.Cellular and molecular life sciences : CMLS · 2026Review
- Accurate Identification of Protein Binding Sites for All Drug Modalities Using ALLSites.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Prediction of Intrinsically Disordered Regions That Bind RNA with DisoRDPbind.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Critical Assessment of Protein Intrinsic Disorder Round 3 - Predicting Disorder in the Era of Protein Language Models.Proteins · 2026Article
- Challenges in Applying DNA-Binding Protein Predictors to Biological Research.International journal of molecular sciences · 2025Article
- Alternate RNA decoding results in stable and abundant proteins in mammals.bioRxiv : the preprint server for biology · 2025Article
- Comparative assessment of binding residue predictions in intrinsically disordered regions.Protein science : a publication of the Protein Society · 2025Article
- Computational Prediction of Linear Interacting Peptides.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Prediction of Intrinsically Disordered Lipid Binding Residues with DisoLipPred.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Prediction of Disordered Linear Interacting Peptides with CLIP.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Prediction of Intrinsic Disorder Functions with DEPICTER2.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Accurate Prediction of Protein-Binding Residues in Protein Sequences Using SCRIBER.Methods in molecular biology (Clifton, N.J.) · 2025Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein-protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/.
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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.