AIMC Topic: RNA-Binding Proteins

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BindUP-Alpha: A Webserver for Predicting DNA-and RNA-binding Proteins based on Experimental and Computational Structural Models☆.

Journal of molecular biology Sep 1, 2025
Structural data provides important information on the proteins' function. Recent development of advanced machine learning and artificial intelligence tools, such as AlphaFold, have led to an explosion of predicted protein structures. However, many of...
Algorithms Protein Binding Computational Biology Software Internet DNA-Binding Proteins Protein Conformation RNA-Binding Proteins Support Vector Machine Models, Molecular
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DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network.

NAR genomics and bioinformatics Jun 1, 2025
Regulation of DNA or RNA at the transcriptional, post-transcriptional, and translational levels are key steps in the central dogma of molecular biology. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) play pivotal roles in the precise reg...
Humans Neural Networks, Computer Software Databases, Protein Deep Learning DNA-Binding Proteins RNA-Binding Proteins
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CR-deal: Explainable Neural Network for circRNA-RBP Binding Site Recognition and Interpretation.

Interdisciplinary sciences, computational life sciences Jun 1, 2025
circRNAs are a type of single-stranded non-coding RNA molecules, and their unique feature is their closed circular structure. The interaction between circRNAs and RNA-binding proteins (RBPs) plays a key role in biological functions and is crucial for...
Neural Networks, Computer RNA, Circular Deep Learning RNA-Binding Proteins Humans Computational Biology Binding Sites
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ASiDentify (ASiD): a machine learning model to predict new autism spectrum disorder risk genes.

Genetics May 8, 2025
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects nearly 3% of children and has a strong genetic component. While hundreds of ASD risk genes have been identified through sequencing studies, the genetic heterogeneity of ASD ...
Machine Learning Autism Spectrum Disorder Genetic Predisposition to Disease Humans RNA-Binding Proteins Neurons
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Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
The interactions between long noncoding RNA (lncRNA) and protein play crucial roles in various biological processes. Computational methods are essential for predicting lncRNA-protein interactions and deciphering their mechanisms. In this chapter, we ...
Proteins Deep Learning Protein Binding RNA-Binding Proteins RNA, Long Noncoding Computational Biology Humans Neural Networks, Computer Software
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Study of prognostic splicing factors in cancer using machine learning approaches.

Human molecular genetics Jun 21, 2024
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing ...
Humans Alternative Splicing Machine Learning RNA Splicing Factors Computational Biology Neoplasms RNA, Messenger Gene Expression Regulation, Neoplastic Prognosis RNA-Binding Proteins Liver Neoplasms RNA Splicing Biomarkers, Tumor Carcinoma, Hepatocellular
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Improved prediction of DNA and RNA binding proteins with deep learning models.

Briefings in bioinformatics May 23, 2024
Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in essential biological processes. To facilitate functional annotation and accurate prediction of different types of NA...
Computational Biology RNA-Binding Proteins DNA-Binding Proteins Humans Neural Networks, Computer Deep Learning
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DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.

Bioinformatics (Oxford, England) Feb 1, 2024
MOTIVATION: Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through intera...
RNA Nucleotide Motifs Humans Computational Biology Animals Deep Learning RNA, Messenger Mice RNA-Binding Proteins
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ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
Position-Specific Scoring Matrices Protein Binding Neural Networks, Computer DNA RNA-Binding Proteins RNA
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PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning.

Bioinformatics (Oxford, England) Apr 12, 2022
MOTIVATION: Protein-RNA interactions play essential roles in many biological processes, including pre-mRNA processing, post-transcriptional gene regulation and RNA degradation. Accurate identification of binding sites on RNA-binding proteins (RBPs) i...
RNA Binding Sites Computational Biology RNA-Binding Proteins Membrane Proteins Deep Learning Protein Binding
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