Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix

Schafer, Jamie L.

doi:10.1016/s0264-410x(98)00173-x

Cited by 98 publications

(58 citation statements)

References 15 publications

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“…As does the diversity of the virus, the diversity of human MHC (HLA) can also pose a challenge to vaccine development. EpiMatrix, [118][119][120][121] an algorithm developed at Brown University and licensed to EpiVax, parses protein sequences into all its possible constituent 9-mer peptides and then estimates the probability of each segment's ability to bind promiscuously to a panel of eight common and representative HLA Class II alleles. Together these eight archetype alleles cover the over 90% of human populations worldwide.…”

Section: Future Directions For Influenza Vaccinesmentioning

confidence: 99%

A call to cellular & humoral arms: Enlisting cognate T cell help to develop broad-spectrum vaccines against influenza A

McMurry¹,

Johansson²,

Groot³

2008

Human Vaccines

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Section: Future Directions For Influenza Vaccinesmentioning

confidence: 99%

A call to cellular & humoral arms: Enlisting cognate T cell help to develop broad-spectrum vaccines against influenza A

McMurry¹,

Johansson²,

Groot³

2008

Human Vaccines

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“…EpiMer and EpiMatrix are computerdriven pattern-matching algorithms that serve to identify T-cellreactive epitopes. Conservatrix and BlastiMer permit the identification of protein sequences for highly conserved regions and homology to other known proteins (257). Although homology-based genomic analysis can yield misleading results in the assignment of gene function (255), it can narrow the list of putative epitopes to be tested.…”

Section: Current and Future Directionsmentioning

confidence: 99%

Coccidioidomycosis: Host Response and Vaccine Development

2004

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Coccidioidomycosis is caused by the dimorphic fungi in the genus Coccidioides. These fungi live as mycelia in the soil of desert areas of the American Southwest, and when the infectious spores, the arthroconidia, are inhaled, they convert into the parasitic spherule/endospore phase. Most infections are mild, but these organisms are frank pathogens and can cause severe lethal disease in fully immunocompetent individuals. While there is increased risk of disseminated disease in certain racial groups and immunocompromised persons, the fact that there are hosts who contain the initial infection and exhibit long-term immunity to reinfection supports the hypothesis that a vaccine against these pathogens is feasible. Multiple studies have shown that protective immunity against primary disease is associated with T-helper 1 (Th-1)-associated immune responses. The single best vaccine in animal models, formalin-killed spherules (FKS), was tested in a human trial but was not found to be significantly protective. This result has prompted studies to better define immunodominant Coccidioides antigen with the thought that a subunit vaccine would be protective. These efforts have defined multiple candidates, but the single best individual immunogen is the protein termed antigen 2/proline-rich antigen (Ag2/PRA). Studies in multiple laboratories have shown that Ag2/PRA as both protein and genetic vaccines provides significant protection against mice challenged systemically with Coccidioides. Unfortunately, compared to the FKS vaccine, it is significantly less protective as measured by both assays of reduction in fungal CFU and assays of survival. The capacity of Ag2/PRA to induce only partial protection was emphasized when animals were challenged intranasally. Thus, there is a need to define new candidates to create a multivalent vaccine to increase the effectiveness of Ag2/PRA. Efforts of genomic screening using expression library immunization or bioinformatic approaches to identify new candidates have revealed at least two new protective proteins, expression library immunization antigen 1 (ELI-Ag1) and a β-1,3-glucanosyltransferase (GEL-1). In addition, previously discovered antigens such as Coccidioides-specific antigen (CSA) should be evaluated in assays of protection. While studies have yet to be completed with combinations of the current candidates, the hypothesis is that with increased numbers of candidates in a multivalent vaccine, there will be increased protection. As the genome sequences of the two Coccidioides strains which are under way are completed and annotated, the effort to find new candidates can increase to provide a complete genomic scan for immunodominant proteins. Thus, much progress has been made in the discovery of subunit vaccine candidates against Coccidioides and there are several candidates showing modest levels of protection, but for complete protection against pulmonary challenge we need to continue the search for additional candidates

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“…potentially immunogenic and worthy of further consideration. In general, we expect about 5% of all assessments to score above 1.64, in any given protein sequence [12]. In several prospective studies, greater than 90% of HLA A2 epitopes predicted using the EpiMatrix HLA A*0201 matrix have been experimentally validated in vitro in multiple studies [8,13,14 …”

Section: Methodsmentioning

confidence: 99%

Immunoinformatic discovery of potential cross-reactive T cell epitopes in the measles genome

Moise

Ardito

Martin

et al. 2011

Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine

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Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix

Cited by 98 publications

References 15 publications

A call to cellular & humoral arms: Enlisting cognate T cell help to develop broad-spectrum vaccines against influenza A

A call to cellular & humoral arms: Enlisting cognate T cell help to develop broad-spectrum vaccines against influenza A

Coccidioidomycosis: Host Response and Vaccine Development

Immunoinformatic discovery of potential cross-reactive T cell epitopes in the measles genome

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