ArticlePloS one2010
Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 609 papers.
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Who cites it
609 citing papers in PubMed.
- Design and in silico evaluation of PV-GNProtecta: an mRNA multi-epitope vaccine candidate against Puumala virus using immunoinformatics and structural analysis.Genomics & informatics · 2026Article
- Immunoinformatics-guided design of a conserved multi-epitope vaccine candidate against pathogenic human coronaviruses.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Targeting Amastigote and Trypomastigote Phases: Multi-Epitope Vaccine Strategy Against Trypanosoma cruzi.Biotechnology and applied biochemistry · 2026Article
- Computational identification of conserved B- and T-cell epitopes for multi-epitope peptide vaccine design against bovine leukemia virus.Virus genes · 2026Article
- Development of a cross-protective subunit cocktail vaccine against diverse serotypes of Glaesserella parasuis infection in pigs.Veterinary research · 2026Article
- Comparative Genomics-Guided Epitope Prioritization and in Silico Design of a Multi-Epitope DNA Vaccine Candidate Against Megalocytivirus pagrus 1.Marine biotechnology (New York, N.Y.) · 2026Article
- Pangenome-GuidedPharmaceuticals (Basel, Switzerland) · 2026Article
- Proteome-Wide Reverse Vaccinology and Immunoinformatics-Guided Design of a Multi-Epitope Vaccine AgainstInternational journal of molecular sciences · 2026Article
- Immunoinformatics Approach for the Designing of a Novel mRNA Vaccine Candidate Against Trypanosoma brucei.Acta parasitologica · 2026Article
- Structure-based immunopharmacological design of a multi-epitope vaccine candidate against Naegleria fowleri targeting TLR3: a pan-genomic and molecular dynamics approach.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Immunopharmacological and structural design of a polyprotein based multi epitope vaccine against Powassan virus.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Integrated immunoinformatics for the design of novel multi-epitope vaccine and identification of new drug targets against Stenotrophomonas maltophilia, a multidrug-resistant superbug.Journal, genetic engineering & biotechnology · 2026Article
- Toward a Vaccine Against Multidrug-Resistant Elizabethkingia anophelis: Comprehensive Immunoinformatics-Based Design of a Multi-Epitope Vaccine and mRNA Construct.Probiotics and antimicrobial proteins · 2026Article
- Structure-Guided Immunoinformatics for the Rational Design of a Multi-Epitope Vaccine Against Batai Orthobunyavirus.Pharmaceuticals (Basel, Switzerland) · 2026Article
- High-throughput in silico multi-epitope reverse vaccine design against hydatidosis.Scientific reports · 2026Article
- Broad-Spectrum Multi-Epitope Design Targeting Conserved Hantavirus Glycoproteins (Gn/Gc): Chimeric Antigen Engineering and Structural Mapping.International journal of molecular sciences · 2026Article
- Immunopharmacological design of a multi-epitope vaccine targeting sarbecovirus Spike glycoprotein.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Immuno-Informatics Design of Multi-Epitope Vaccine Candidate AgainstHealth science reports · 2026Article
- Immunopharmacologsical and structural insights into Rift Valley fever virus envelope glycoproteins: an immunoinformatics approach to multi-epitope vaccine design.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Computational Design of a Broad-Spectrum Multi-Epitope mRNA Vaccine Candidate for Mammarenaviruses.Applied biochemistry and biotechnology · 2026Article
549 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response, C-ImmSim, such that it represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction. This is a key step for the simulation of the immune response, because it determines immunogenicity. The binding of the epitope, which is the immunogenic part of an invading pathogen, together with activation and cooperation from T helper cells, is required to trigger an immune response in the affected host. To determine a pathogen's epitopes, we use existing prediction methods. In addition, we propose a novel method, which uses Miyazawa and Jernigan protein-protein potential measurements, for assessing molecular binding in the context of immune complexes. We benchmark the resulting model by simulating a classical immunization experiment that reproduces the development of immune memory. We also investigate the role of major histocompatibility complex (MHC) haplotype heterozygosity and homozygosity with respect to the influenza virus and show that there is an advantage to heterozygosity. Finally, we investigate the emergence of one or more dominating clones of lymphocytes in the situation of chronic exposure to the same immunogenic molecule and show that high affinity clones proliferate more than any other. These results show that the simulator produces dynamics that are stable and consistent with basic immunological knowledge. We believe that the combination of genomic information and simulation of the dynamics of the immune system, in one single tool, can offer new perspectives for a better understanding of the immune system.
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