AIMC Topic: Protein Isoforms

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Prediction of Cytochrome P450 Inhibition Using a Deep Learning Approach and Substructure Pattern Recognition.

Journal of chemical information and modeling Oct 21, 2023
Cytochrome P450 (CYP) is a family of enzymes that are responsible for about 75% of all metabolic reactions. Among them, CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 participate in the metabolism of most drugs and mediate many adverse drug reactions. T...
Microsomes, Liver Cytochrome P-450 Enzyme System Cytochrome P-450 CYP3A Deep Learning Cytochrome P-450 Enzyme Inhibitors Cytochrome P-450 CYP2D6 Cytochrome P-450 CYP1A2 Cytochrome P-450 CYP2C19 Cytochrome P-450 CYP2C9 Protein Isoforms
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DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
Alternative splicing enables a gene translating into different isoforms and into the corresponding proteoforms, which actually accomplish various biological functions of a living body. Isoform-isoform interactions (IIIs) provide a higher resolution i...
Neural Networks, Computer Humans Protein Isoforms Alternative Splicing
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DeepIDA: Predicting Isoform-Disease Associations by Data Fusion and Deep Neural Networks.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
Alternative splicing produces different isoforms from the same gene locus, it is an important mechanism for regulating gene expression and proteome diversity. Although the prediction of gene(ncRNA)-disease associations has been extensively studied, f...
Neural Networks, Computer Alternative Splicing Computational Biology Proteome Protein Isoforms Gene Ontology
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Using machine learning to detect the differential usage of novel gene isoforms.

BMC bioinformatics Jan 18, 2022
BACKGROUND: Differential isoform usage is an important driver of inter-individual phenotypic diversity and is linked to various diseases and traits. However, accurately detecting the differential usage of different gene transcripts between groups can...
Sequence Analysis, RNA Protein Isoforms Exons Machine Learning Gene Expression Profiling Alternative Splicing
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PIC-Me: paralogs and isoforms classifier based on machine-learning approaches.

BMC bioinformatics Oct 21, 2021
BACKGROUND: Paralogs formed through gene duplication and isoforms formed through alternative splicing have been important processes for increasing protein diversity and maintaining cellular homeostasis. Despite their recognized importance and the adv...
Alternative Splicing Machine Learning Protein Isoforms Sequence Alignment Molecular Sequence Annotation
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Improved prediction of smoking status via isoform-aware RNA-seq deep learning models.

PLoS computational biology Oct 11, 2021
Most predictive models based on gene expression data do not leverage information related to gene splicing, despite the fact that splicing is a fundamental feature of eukaryotic gene expression. Cigarette smoking is an important environmental risk fac...
Smoking Protein Isoforms Exons Computational Biology Models, Statistical Middle Aged Gene Expression Profiling ROC Curve RNA-Seq Deep Learning Female Aged Male Humans
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DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms.

BMC bioinformatics Jan 18, 2021
BACKGROUND: Long non-coding RNAs (lncRNAs) regulate diverse biological processes via interactions with proteins. Since the experimental methods to identify these interactions are expensive and time-consuming, many computational methods have been prop...
Protein Isoforms RNA, Long Noncoding Neural Networks, Computer Mice Deep Learning Animals Computational Biology
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A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data.

Methods (San Diego, Calif.) Jun 10, 2020
MOTIVATION: Alternative splicing makes significant contributions to functional diversity of transcripts and proteins. Many alternatively spliced gene isoforms have been shown to perform specific biological functions under different contexts. In addit...
High-Throughput Nucleotide Sequencing Gene Expression Regulation Exons Alternative Splicing Protein Isoforms Software Computational Biology Sequence Analysis, RNA Humans Neural Networks, Computer
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ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches.

Journal of chemical information and modeling Nov 5, 2019
Adverse effects induced by drug-drug interactions may result in early termination of drug development or even withdrawal of drugs from the market, and many drug-drug interactions are caused by the inhibition of cytochrome P450 (CYP450) enzymes. There...
Machine Learning Algorithms Drug Discovery Humans Quantitative Structure-Activity Relationship Neural Networks, Computer Protein Isoforms Artificial Intelligence Models, Biological Cytochrome P-450 Enzyme Inhibitors Cytochrome P-450 Enzyme System
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Prediction of Human Cytochrome P450 Inhibition Using a Multitask Deep Autoencoder Neural Network.

Molecular pharmaceutics May 30, 2018
Adverse side effects of drug-drug interactions induced by human cytochrome P450 (CYP450) inhibition is an important consideration in drug discovery. It is highly desirable to develop computational models that can predict the inhibitive effect of a co...
Cytochrome P-450 Enzyme System Quantitative Structure-Activity Relationship Cytochrome P-450 Enzyme Inhibitors Protein Isoforms Machine Learning Humans Algorithms Neural Networks, Computer Drug Interactions
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