AIMC Topic: Epitopes

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Ab-initio conformational epitope structure prediction using genetic algorithm and SVM for vaccine design.

Computer methods and programs in biomedicine Oct 12, 2017
BACKGROUND AND OBJECTIVE: T-cell epitope structure identification is a significant challenging immunoinformatic problem within epitope-based vaccine design. Epitopes or antigenic peptides are a set of amino acids that bind with the Major Histocompati...
T-Lymphocytes ROC Curve Support Vector Machine Area Under Curve Humans Algorithms Epitopes Vaccines
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Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules.

Immunology Jun 19, 2017
MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or les...
Protein Interaction Domains and Motifs Histocompatibility Antigens Class II Protein Binding Computational Biology Humans Structure-Activity Relationship Epitopes Databases, Protein Neural Networks, Computer Mutation Antibodies, Monoclonal Ligands Machine Learning Binding Sites Peptides
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and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes.

The Journal of biological chemistry May 23, 2017
Tumor exomes provide comprehensive information on mutated, overexpressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T-cell epitopes, because neoepitope-s...
Cancer Vaccines Antigens, Neoplasm Vaccines, Synthetic Membrane Proteins Melanoma Reproducibility of Results Animals Computational Biology HLA-A2 Antigen Protein Stability Expert Systems Oligopeptides Immunogenicity, Vaccine Neoplasm Proteins Mice, Knockout Peptide Fragments Epitopes Humans Artificial Intelligence Cells, Cultured Mice, Transgenic Models, Immunological Protein Refolding T-Lymphocytes, Cytotoxic
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Enhancing the Biological Relevance of Machine Learning Classifiers for Reverse Vaccinology.

International journal of molecular sciences Feb 1, 2017
Reverse vaccinology (RV) is a bioinformatics approach that can predict antigens with protective potential from the protein coding genomes of bacterial pathogens for subunit vaccine design. RV has become firmly established following the development of...
Mutagenesis Antigens, Bacterial Bacterial Vaccines Epitope Mapping Vaccines, Subunit Support Vector Machine Area Under Curve Bacterial Proteins Epitopes Humans Machine Learning ROC Curve Computational Biology
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Improved pan-specific prediction of MHC class I peptide binding using a novel receptor clustering data partitioning strategy.

HLA Oct 20, 2016
Pan-specific prediction of receptor-ligand interaction is conventionally done using machine-learning methods that integrates information about both receptor and ligand primary sequences. To achieve optimal performance using machine learning, dealing ...
Humans Histocompatibility Antigens Class I Ligands Oligopeptides Mice Binding Sites Machine Learning Protein Interaction Domains and Motifs Macaca Gene Expression Software Structural Homology, Protein Epitopes Animals Gorilla gorilla Protein Binding Pan troglodytes Alleles
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An ontology for major histocompatibility restriction.

Journal of biomedical semantics Jan 11, 2016
BACKGROUND: MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in ...
Animals Databases, Protein HLA Antigens Epitopes Gene Ontology Major Histocompatibility Complex Histocompatibility Antigens Humans Software
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Gapped sequence alignment using artificial neural networks: application to the MHC class I system.

Bioinformatics (Oxford, England) Oct 29, 2015
MOTIVATION: Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to pep...
Histocompatibility Antigens Class I Sequence Alignment Protein Binding Computational Biology Peptide Fragments Humans Epitopes Neural Networks, Computer Algorithms
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Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

Immunogenetics Sep 29, 2015
A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented ...
Cluster Analysis Databases, Protein Models, Molecular Peptide Fragments Animals Humans Sequence Homology, Amino Acid Epitopes Protein Binding Neural Networks, Computer Amino Acid Sequence Histocompatibility Antigens Class II Mice Algorithms Binding Sites Molecular Sequence Data Computational Biology
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High-order neural networks and kernel methods for peptide-MHC binding prediction.

Bioinformatics (Oxford, England) Jul 23, 2015
MOTIVATION: Effective computational methods for peptide-protein binding prediction can greatly help clinical peptide vaccine search and design. However, previous computational methods fail to capture key nonlinear high-order dependencies between diff...
ROC Curve Major Histocompatibility Complex Area Under Curve Humans Epitopes Neural Networks, Computer Protein Binding Amino Acid Sequence Support Vector Machine Algorithms Molecular Sequence Data Databases, Protein Peptides
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Geometric epitope and paratope prediction.

Bioinformatics (Oxford, England) Jul 1, 2024
MOTIVATION: Identifying the binding sites of antibodies is essential for developing vaccines and synthetic antibodies. In this article, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the ...
Computational Biology Antibodies Software Epitopes Deep Learning Protein Conformation Binding Sites
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