ReviewInternational journal of molecular sciences2015
An overview of the prediction of protein DNA-binding sites.
Review in International journal of molecular sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- TripleBind: a generalizable deep learning framework for protein-nucleic acid and protein-ligand binding sites prediction based on pre-trained protein language models.Molecular diversity · 2026Article
- PRIMED: predicting DNA binding residues by leveraging pre-trained protein language models.Frontiers in artificial intelligence · 2026Article
- PTF-Vāc: An explainable and generative deep co-learning encoder-decoder system for ab initio discovery of plant transcription factor binding sites.Plant communications · 2025Article
- ProGraphTrans: multimodal dynamic collaborative framework for protein representation learning.BMC biology · 2025Article
- TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning.Communications biology · 2025Article
- A Survey of Deep Learning Methods and Tools for Protein Binding Site Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Advances in Language-Model-Informed Protein-Nucleic Acid Binding Site Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- DescribePROT Database of Residue-Level Protein Structure and Function Annotations.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Binding of MAP3773c Protein ofInternational journal of molecular sciences · 2024Article
- Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.Briefings in bioinformatics · 2024Review
- Deep Learning-Based Classification of Histone-DNA Interactions Using Drying Droplet Patterns.Small science · 2024Article
- Structure-based prediction of protein-nucleic acid binding using graph neural networks.Biophysical reviews · 2024Review
- Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response.Molecular biotechnology · 2024Article
- HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins.Nucleic acids research · 2024Article
- PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features.Methods (San Diego, Calif.) · 2023Article
- CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach.Journal of fungi (Basel, Switzerland) · 2023Article
- Mass Spectrometry for Assessing Protein-Nucleic Acid Interactions.Analytical chemistry · 2023Review
- qNABpredict: Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids.Protein science : a publication of the Protein Society · 2023Article
- Availability of web servers significantly boosts citations rates of bioinformatics methods for protein function and disorder prediction.Bioinformatics advances · 2023Article
- Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding sites. We also propose specific implications that are likely to result in novel prediction methods, increased performance, or practical applications.
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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.