AIMC Topic: Antigens

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TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning.

Nucleic acids research
The cellular immune system, which is a critical component of human immunity, uses T cell receptors (TCRs) to recognize antigenic proteins in the form of peptides presented by major histocompatibility complex (MHC) proteins. Accurate definition of the...

Vaxi-DL: An Artificial Intelligence-Enabled Platform for Vaccine Development.

Methods in molecular biology (Clifton, N.J.)
Vaccine development is a complex and long process. It involves several steps, including computational studies, experimental analyses, animal model system studies, and clinical trials. This process can be accelerated by using in silico antigen screeni...

Paragraph-antibody paratope prediction using graph neural networks with minimal feature vectors.

Bioinformatics (Oxford, England)
SUMMARY: The development of new vaccines and antibody therapeutics typically takes several years and requires over $1bn in investment. Accurate knowledge of the paratope (antibody binding site) can speed up and reduce the cost of this process by impr...

Contemporary Challenges in Clinical Flow Cytometry: Small Samples, Big Data, Little Time.

The journal of applied laboratory medicine
BACKGROUND: Immunophenotypic analysis of cell populations by flow cytometry has an established role in primary diagnosis and disease monitoring of many hematologic diseases. A persistent problem in evaluation of specimens is suboptimal cell counts an...

DLAB: deep learning methods for structure-based virtual screening of antibodies.

Bioinformatics (Oxford, England)
MOTIVATION: Antibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time- and ...

Precision immunoprofiling to reveal diagnostic signatures for latent tuberculosis infection and reactivation risk stratification.

Integrative biology : quantitative biosciences from nano to macro
Latent tuberculosis infection (LTBI) is estimated in nearly one quarter of the world's population, and of those immunocompetent and infected ~10% will proceed to active tuberculosis (TB). Current diagnostics cannot definitively identify LTBI and prov...

Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information.

Annals of oncology : official journal of the European Society for Medical Oncology
BACKGROUND: Tumor-specific mutations form novel immunogenic peptides called neoantigens. Neoantigens can be used as a biomarker predicting patient response to cancer immunotherapy. Although a predicted binding affinity (IC50) between peptide and majo...