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Proteomics

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An individualized protein-based prognostic model to stratify pediatric patients with papillary thyroid carcinoma.

Nature communications
Pediatric papillary thyroid carcinomas (PPTCs) exhibit high inter-tumor heterogeneity and currently lack widely adopted recurrence risk stratification criteria. Hence, we propose a machine learning-based objective method to individually predict their...

Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells.

Science (New York, N.Y.)
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advan...

A Review for Artificial Intelligence Based Protein Subcellular Localization.

Biomolecules
Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer's disease. Knowing where a target protein re...

Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network.

Talanta
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and hig...

Proteomics landscape and machine learning prediction of long-term response to splenectomy in primary immune thrombocytopenia.

British journal of haematology
This study aimed to identify key proteomic analytes correlated with response to splenectomy in primary immune thrombocytopenia (ITP). Thirty-four patients were retrospectively collected in the training cohort and 26 were prospectively enrolled as val...

Prediction of glycopeptide fragment mass spectra by deep learning.

Nature communications
Deep learning has achieved a notable success in mass spectrometry-based proteomics and is now emerging in glycoproteomics. While various deep learning models can predict fragment mass spectra of peptides with good accuracy, they cannot cope with the ...

In-depth discovery and taste presentation mechanism studies on umami peptides derived from fermented sea bass based on peptidomics and machine learning.

Food chemistry
Umami peptides originating from fermented sea bass impart a distinctive flavor to food. Nevertheless, large-scale and rapid screening for umami peptides using conventional techniques is challenging because of problems such as prolonged duration and c...

A Comprehensive Review on Machine Learning Techniques for Protein Family Prediction.

The protein journal
Proteomics is a field dedicated to the analysis of proteins in cells, tissues, and organisms, aiming to gain insights into their structures, functions, and interactions. A crucial aspect within proteomics is protein family prediction, which involves ...

Personalized Drug Therapy: Innovative Concept Guided With Proteoformics.

Molecular & cellular proteomics : MCP
Personalized medicine can reduce adverse effects, enhance drug efficacy, and optimize treatment outcomes, which represents the essence of personalized medicine in the pharmacy field. Protein drugs are crucial in the field of personalized drug therapy...

Artificial intelligence for drug discovery and development in Alzheimer's disease.

Current opinion in structural biology
The complex molecular mechanism and pathophysiology of Alzheimer's disease (AD) limits the development of effective therapeutics or prevention strategies. Artificial Intelligence (AI)-guided drug discovery combined with genetics/multi-omics (genomics...