AIMC Topic: Spike Glycoprotein, Coronavirus

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Computationally designed proteins mimic antibody immune evasion in viral evolution.

Immunity Jun 10, 2025
Recurrent waves of viral infection necessitate vaccines and therapeutics that remain effective against emerging viruses. Our ability to evaluate interventions is currently limited to assessments against past or circulating variants, which likely diff...
Antibodies, Viral Antibodies, Neutralizing SARS-CoV-2 Spike Glycoprotein, Coronavirus Humans Animals Angiotensin-Converting Enzyme 2 COVID-19 Evolution, Molecular COVID-19 Vaccines Immune Evasion
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Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules.

The journal of physical chemistry. B Jun 5, 2025
Machine learning (ML) techniques have become powerful tools in both industrial and academic settings. Their ability to facilitate analysis of complex data and generation of predictive insights is transforming how scientific problems are approached ac...
Humans Spike Glycoprotein, Coronavirus Molecular Dynamics Simulation Angiotensin-Converting Enzyme 2 Machine Learning SARS-CoV-2 Protein Binding
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Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.

Nucleic acids research Feb 8, 2025
In infected individuals, viruses are present as a population consisting of dominant and minor variant genomes. Most databases contain information on the dominant genome sequence. Since the emergence of SARS-CoV-2 in late 2019, variants have been sele...
Mutation SARS-CoV-2 Genome, Viral Spike Glycoprotein, Coronavirus Humans Evolution, Molecular Machine Learning COVID-19
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Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.

Briefings in bioinformatics Sep 23, 2024
The COVID-19 pandemic is marked by the successive emergence of new SARS-CoV-2 variants, lineages, and sublineages that outcompete earlier strains, largely due to factors like increased transmissibility and immune escape. We propose DeepAutoCoV, an un...
SARS-CoV-2 Deep Learning Spike Glycoprotein, Coronavirus Pandemics Humans COVID-19 Forecasting
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Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.

GigaScience Jan 2, 2024
Identification of protein-protein and protein-nucleic acid binding sites provides insights into biological processes related to protein functions and technical guidance for disease diagnosis and drug design. However, accurate predictions by computati...
Humans Neural Networks, Computer COVID-19 Spike Glycoprotein, Coronavirus Computational Biology Nucleic Acids SARS-CoV-2 Deep Learning Protein Binding Binding Sites
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Unraveling viral drug targets: a deep learning-based approach for the identification of potential binding sites.

Briefings in bioinformatics Nov 22, 2023
The coronavirus disease 2019 (COVID-19) pandemic has spurred a wide range of approaches to control and combat the disease. However, selecting an effective antiviral drug target remains a time-consuming challenge. Computational methods offer a promisi...
Spike Glycoprotein, Coronavirus Molecular Dynamics Simulation Binding Sites Humans COVID-19 SARS-CoV-2 Deep Learning Protein Binding Antibodies, Viral
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HLAncPred: a method for predicting promiscuous non-classical HLA binding sites.

Briefings in bioinformatics Sep 20, 2022
Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional ...
Spike Glycoprotein, Coronavirus Binding Sites HLA-G Antigens Peptides Protein Binding Humans Artificial Intelligence COVID-19
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Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants.

Briefings in bioinformatics May 13, 2022
Explosively emerging SARS-CoV-2 variants challenge current nomenclature schemes based on genetic diversity and biological significance. Genomic composition-based machine learning methods have recently performed well in identifying phenotype-genotype ...
Child COVID-19 Humans Spike Glycoprotein, Coronavirus SARS-CoV-2 Mutation Deep Learning
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Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2.

Proceedings of the National Academy of Sciences of the United States of America Oct 19, 2021
The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 ha...
Neural Networks, Computer SARS-CoV-2 Spike Glycoprotein, Coronavirus Molecular Dynamics Simulation Host-Pathogen Interactions Angiotensin-Converting Enzyme 2 Humans Amino Acid Substitution Binding Sites
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Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning.

Nucleic acids research Jul 2, 2021
Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-bas...
Antigens, Viral Vaccinology Software Workflow COVID-19 Proteome Vaccines SARS-CoV-2 Epitopes Internet Humans Drug Design Machine Learning COVID-19 Vaccines Spike Glycoprotein, Coronavirus
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