Single-stranded DNA binding proteins and their identification using machine learning-based approaches

JT Guo, F Malik - Biomolecules, 2022 - mdpi.com
Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome
stability by protecting the transient existence of ssDNA from damage during essential …

DeepFeature: feature selection in nonimage data using convolutional neural network

A Sharma, A Lysenko, KA Boroevich… - Briefings in …, 2021 - academic.oup.com
Artificial intelligence methods offer exciting new capabilities for the discovery of biological
mechanisms from raw data because they are able to detect vastly more complex patterns of …

CNN-Pred: Prediction of single-stranded and double-stranded DNA-binding protein using convolutional neural networks

F Manavi, A Sharma, R Sharma, T Tsunoda… - Gene, 2023 - Elsevier
DNA-binding proteins play a vital role in biological activity including DNA replication, DNA
packing, and DNA reparation. DNA-binding proteins can be classified into single-stranded …

DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences

J Zhang, S Ghadermarzi, A Katuwawala… - Briefings in …, 2021 - academic.oup.com
Efforts to elucidate protein–DNA interactions at the molecular level rely in part on accurate
predictions of DNA-binding residues in protein sequences. While there are over a dozen …

Reduced cellular process and developmental process genotoxicity of polystyrene nanoplastics in zebrafish embryogenesis using Aurelia aurita proteins

IH Park, SW Geum, MK Yeo - Molecular & Cellular Toxicology, 2023 - Springer
Background The effects of polystyrene nanoplastic (PS-NP) on the human body is a matter
of global concern, as they are mainly absorbed through the food chain after release into the …

Rudeus, a machine learning classification system to study dna-binding proteins

D Medina-Ortiz, G Cabas-Mora, I Moya-Barria… - bioRxiv, 2024 - biorxiv.org
DNA-binding proteins are essential in different biological processes, including DNA
replication, transcription, packaging, and chromatin remodelling. Exploring their …

Genome-wide identification and characterization of the sweet orange (Citrus sinensis) basic helix-loop-helix (bHLH) family reveals a role for CsbHLH085 as a …

X Huang, L Su, B Xian, Q Yu, M Zhang, J Fan… - International Journal of …, 2024 - Elsevier
Citrus bacterial canker (CBC) is a harmful bacterial disease caused by Xanthomonas citri
subsp. citri (Xcc), negatively impacting citrus production worldwide. The basic helix-loop …

Integrating reduced amino acid composition into PSSM for improving copper ion-binding protein prediction

S Liu, Y Liang, J Li, S Yang, M Liu, C Liu… - International Journal of …, 2023 - Elsevier
Copper ion-binding proteins play an essential role in metabolic processes and are critical
factors in many diseases, such as breast cancer, lung cancer, and Menkes disease. Many …

Improved prediction of DNA and RNA binding proteins with deep learning models

S Wu, J Guo - Briefings in Bioinformatics, 2024 - academic.oup.com
Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-
binding proteins (RBPs), play important roles in essential biological processes. To facilitate …

A novel prediction method for protein DNA-binding residues based on neighboring residue correlations

J Song, G Liu, J Jiang - Biotechnology & Biotechnological …, 2022 - Taylor & Francis
Accurately identifying the protein DNA-binding residues is important for understanding the
protein–DNA recognition mechanism and protein function annotation. Many computational …