AIMC Topic: Proteome
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Protein Condensate Atlas from predictive models of heteromolecular condensate composition.
Nature communications
Jul 10, 2024
Biomolecular condensates help cells organise their content in space and time. Cells harbour a variety of condensate types with diverse composition and many are likely yet to be discovered. Here, we develop a methodology to predict the composition of ...
TriplEP-CPP: Algorithm for Predicting the Properties of Peptide Sequences.
International journal of molecular sciences
Jun 22, 2024
Advancements in medicine and pharmacology have led to the development of systems that deliver biologically active molecules inside cells, increasing drug concentrations at target sites. This improves effectiveness and duration of action and reduces s...
Computational design of soluble and functional membrane protein analogues.
Nature
Jun 19, 2024
De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topolog...
Deep-learning-enabled antibiotic discovery through molecular de-extinction.
Nature biomedical engineering
Jun 11, 2024
Molecular de-extinction aims at resurrecting molecules to solve antibiotic resistance and other present-day biological and biomedical problems. Here we show that deep learning can be used to mine the proteomes of all available extinct organisms for t...
Protein function annotation and virulence factor identification of Klebsiella pneumoniae genome by multiple machine learning models.
Microbial pathogenesis
Jun 6, 2024
Klebsiella pneumoniae is a type of Gram-negative bacterium which can cause a range of infections in human. In recent years, an increasing number of strains of K. pneumoniae resistant to multiple antibiotics have emerged, posing a significant threat t...
Folding the human proteome using BioNeMo: A fused dataset of structural models for machine learning purposes.
Scientific data
Jun 6, 2024
Human proteins are crucial players in both health and disease. Understanding their molecular landscape is a central topic in biological research. Here, we present an extensive dataset of predicted protein structures for 42,042 distinct human proteins...
Alzheimer's disease early screening and staged detection with plasma proteome using machine learning and convolutional neural network.
The European journal of neuroscience
May 19, 2024
Alzheimer's disease (AD) stands as the prevalent progressive neurodegenerative disease, precipitating cognitive impairment and even memory loss. Amyloid biomarkers have been extensively used in the diagnosis of AD. However, amyloid proteins offer lim...
An individualized protein-based prognostic model to stratify pediatric patients with papillary thyroid carcinoma.
Nature communications
Apr 26, 2024
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.)
Apr 26, 2024
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...
Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens.
Vaccine
Mar 23, 2024
Vaccines have significantly reduced the impact of numerous deadly viral infections. However, there is an increasing need to expedite vaccine development in light of the recurrent pandemics and epidemics. Also, identifying vaccines against certain vir...
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