AIMC Topic: Epitopes
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Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens.
Journal of chemical theory and computation
Aug 1, 2023
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeut...
Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models.
Methods in enzymology
Dec 8, 2022
Antibodies are an established class of human therapeutics. Epitope characterization is an important part of therapeutic antibody discovery. However, structural characterization of antibody-antigen complexes remains challenging. On the one hand, X-ray...
Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics.
Nature communications
Jun 7, 2021
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of non-tryptic peptides presents substantial computational...
Improvement of Neoantigen Identification Through Convolution Neural Network.
Frontiers in immunology
May 25, 2021
Accurate prediction of neoantigens and the subsequent elicited protective anti-tumor response are particularly important for the development of cancer vaccine and adoptive T-cell therapy. However, current algorithms for predicting neoantigens are lim...
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information.
BMC bioinformatics
May 5, 2021
BACKGROUND: Epitope prediction is a useful approach in cancer immunology and immunotherapy. Many computational methods, including machine learning and network analysis, have been developed quickly for such purposes. However, regarding clinical applic...
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification.
PLoS computational biology
Mar 29, 2021
High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in...
Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning.
Frontiers in immunology
Feb 10, 2021
The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achie...
Hepatitis C Antigens
Peptide Library
Peptide Fragments
Epitopes
AIDS Serodiagnosis
Machine Learning
Oligonucleotides
DNA Barcoding, Taxonomic
Amino Acid Sequence
Humans
Antigen-Antibody Reactions
Communicable Diseases
HIV Core Protein p24
Hepatitis C
Base Sequence
DNA, Recombinant
HIV Infections
Genetic Vectors
Serologic Tests
Polymerase Chain Reaction
HIV Envelope Protein gp160
HIV Antibodies
High-Throughput Nucleotide Sequencing
Hepatitis C Antibodies
Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy.
BMC bioinformatics
Dec 30, 2020
BACKGROUND: Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in cancer cells lead to tumor r...
Machine learning-guided evolution of BMP-2 knuckle Epitope-Derived osteogenic peptides to target BMP receptor II.
Journal of drug targeting
May 1, 2020
Bone morphogenetic protein-2 (BMP-2) is a key regulator of bone formation, growth and regeneration, which contains a conformational wrist epitope and a linear knuckle epitope that are functionally responsible for the protein by mediating its interact...
A novel algorithm to improve specificity in ovarian cancer detection.
Cancer treatment and research communications
Nov 10, 2017
BACKGROUND: Measurement of autoantibodies (AAbs) to tumor associated antigens has been proposed to aid in the early detection of ovarian cancer with high specificity. Here we describe a multiplex approach to evaluate selected peptide epitopes of p53 ...
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