AIMC Topic: Epitopes
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Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach.
Journal of computer-aided molecular design
May 26, 2025
Rickettsia is a genus of bacteria that are obligate intracellular parasites and are responsible for the febrile diseases known collectively as Rickettsioses. The emergence of antibiotic resistance is an escalating concern and thus developing a vaccin...
Machine learning models for predicting configuration of modified knuckle epitope peptides of BMP-2 protein using mesoscale simulation data.
Physical chemistry chemical physics : PCCP
Apr 30, 2025
The high doses of bone morphogenetic proteins (BMPs) cause undesired side effects in skeletal tissue regeneration. An alternative approach is to use the bioactive knuckle epitope domain of BMP-2 (BMP2-KEP) with an open-arm structure as part of the pr...
Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.
PLoS computational biology
Apr 21, 2025
The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a complementarity-determining region (CDR) grafting appro...
Deep mutational learning for the selection of therapeutic antibodies resistant to the evolution of Omicron variants of SARS-CoV-2.
Nature biomedical engineering
Mar 5, 2025
Most antibodies for treating COVID-19 rely on binding the receptor-binding domain (RBD) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). However, Omicron and its sub-lineages, as well as other heavily mutated variants, have rendered m...
RAG_MCNNIL6: A Retrieval-Augmented Multi-Window Convolutional Network for Accurate Prediction of IL-6 Inducing Epitopes.
Journal of chemical information and modeling
Feb 19, 2025
Interleukin-6 (IL-6) is a critical cytokine involved in immune regulation, inflammation, and the pathogenesis of various diseases, including autoimmune disorders, cancer, and the cytokine storm associated with severe COVID-19. Identifying IL-6 induci...
NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface.
BMC bioinformatics
Dec 18, 2024
BACKGROUND: Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens gen...
Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning.
PLoS computational biology
Nov 20, 2024
The ability to predict HIV-1 resistance to broadly neutralizing antibodies (bnAbs) will increase bnAb therapeutic benefits. Machine learning is a powerful approach for such prediction. One challenge is that some HIV-1 subtypes in currently available ...
Machine learning accelerates the discovery of epitope-based dual-bioactive peptides against skin infections.
International journal of antimicrobial agents
Oct 31, 2024
OBJECTIVES: Skin injuries and infections are an inevitable part of daily human life, particularly with chronic wounds, becoming an increasing socioeconomic burden. In treating skin infections and promoting wound healing, bioactive peptides may hold s...
Integrating machine learning to advance epitope mapping.
Frontiers in immunology
Sep 30, 2024
Identifying epitopes, or the segments of a protein that bind to antibodies, is critical for the development of a variety of immunotherapeutics and diagnostics. In vaccine design, the intent is to identify the minimal epitope of an antigen that can el...
Machine-learning-assisted high-throughput identification of potent and stable neutralizing antibodies against all four dengue virus serotypes.
Scientific reports
Jul 26, 2024
Several computational methods have been developed to identify neutralizing antibodies (NAbs) covering four dengue virus serotypes (DENV-1 to DENV-4); however, limitations of the dataset and the resulting performance remain. Here, we developed a new c...
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