ArticlePloS one2014
iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed, 312 citations in OpenAlex.
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- Benchmarking recent computational tools for DNA-binding protein identification.Briefings in bioinformatics · 2024Article
- Systematic discovery of DNA-binding tandem repeat proteins.Nucleic acids research · 2024Article
- AMP-RNNpro: a two-stage approach for identification of antimicrobials using probabilistic features.Scientific reports · 2024Article
- ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.Protein science : a publication of the Protein Society · 2024Article
- Protein feature engineering framework for AMPylation site prediction.Scientific reports · 2024Article
- StackDPP: a stacking ensemble based DNA-binding protein prediction model.BMC bioinformatics · 2024Article
- Deep-WET: a deep learning-based approach for predicting DNA-binding proteins using word embedding techniques with weighted features.Scientific reports · 2024Article
- PreTP-2L: identification of therapeutic peptides and their types using two-layer ensemble learning framework.Bioinformatics (Oxford, England) · 2023Article
- Align-gram: Rethinking the Skip-gram Model for Protein Sequence Analysis.The protein journal · 2023Article
- Accurately identifying hemagglutinin using sequence information and machine learning methods.Frontiers in medicine · 2023Article
- FTWSVM-SR: DNA-Binding Proteins Identification via Fuzzy Twin Support Vector Machines on Self-Representation.Interdisciplinary sciences, computational life sciences · 2022Article
- Research progress of reduced amino acid alphabets in protein analysis and prediction.Computational and structural biotechnology journal · 2022Review
- Hybrid_DBP: Prediction of DNA-binding proteins using hybrid features and convolutional neural networks.Frontiers in pharmacology · 2022Article
- DBP-iDWT: Improving DNA-Binding Proteins Prediction Using Multi-Perspective Evolutionary Profile and Discrete Wavelet Transform.Computational intelligence and neuroscience · 2022Article
44 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Playing crucial roles in various cellular processes, such as recognition of specific nucleotide sequences, regulation of transcription, and regulation of gene expression, DNA-binding proteins are essential ingredients for both eukaryotic and prokaryotic proteomes. With the avalanche of protein sequences generated in the postgenomic age, it is a critical challenge to develop automated methods for accurate and rapidly identifying DNA-binding proteins based on their sequence information alone. Here, a novel predictor, called "iDNA-Prot|dis", was established by incorporating the amino acid distance-pair coupling information and the amino acid reduced alphabet profile into the general pseudo amino acid composition (PseAAC) vector. The former can capture the characteristics of DNA-binding proteins so as to enhance its prediction quality, while the latter can reduce the dimension of PseAAC vector so as to speed up its prediction process. It was observed by the rigorous jackknife and independent dataset tests that the new predictor outperformed the existing predictors for the same purpose. As a user-friendly web-server, iDNA-Prot|dis is accessible to the public at http://bioinformatics.hitsz.edu.cn/iDNA-Prot_dis/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step protocol guide is provided on how to use the web-server to get their desired results without the need to follow the complicated mathematic equations that are presented in this paper just for the integrity of its developing process. It is anticipated that the iDNA-Prot|dis predictor may become a useful high throughput tool for large-scale analysis of DNA-binding proteins, or at the very least, play a complementary role to the existing predictors in this regard.
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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.