ArticleNucleic acids research2014
NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Neutralization Sensitivity and Evolution of Virus in a Chronic HIV-1 Clade B Infected Patient with Neutralizing Activity against Membrane-Proximal External Region.Pathogens (Basel, Switzerland) · 2023Article
- Vertical HIV-1 Transmission in the Setting of Maternal Broad and Potent Antibody Responses.Journal of virology · 2022Article
- Neutralization Sensitivity of HIV-1 CRF07_BC From an Untreated Patient With a Focus on Evolution Over Time.Frontiers in cellular and infection microbiology · 2022Article
- SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens.Nucleic acids research · 2019Article
- Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.PLoS computational biology · 2019Article
- HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design.Cell host & microbe · 2019Article
- Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1.Immunological reviews · 2017Review
- Virologic effects of broadly neutralizing antibody VRC01 administration during chronic HIV-1 infection.Science translational medicine · 2015Article
- The Anopheles-midgut APN1 structure reveals a new malaria transmission-blocking vaccine epitope.Nature structural & molecular biology · 2015Article
- CATNAP: a tool to compile, analyze and tally neutralizing antibody panels.Nucleic acids research · 2015Article
- PyIgClassify: a database of antibody CDR structural classifications.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Delineation of the antigenic site, or epitope, recognized by an antibody can provide clues about functional vulnerabilities and resistance mechanisms, and can therefore guide antibody optimization and epitope-based vaccine design. Previously, we developed an algorithm for antibody-epitope prediction based on antibody neutralization of viral strains with diverse sequences and validated the algorithm on a set of broadly neutralizing HIV-1 antibodies. Here we describe the implementation of this algorithm, NEP (Neutralization-based Epitope Prediction), as a web-based server. The users must supply as input: (i) an alignment of antigen sequences of diverse viral strains; (ii) neutralization data for the antibody of interest against the same set of antigen sequences; and (iii) (optional) a structure of the unbound antigen, for enhanced prediction accuracy. The prediction results can be downloaded or viewed interactively on the antigen structure (if supplied) from the web browser using a JSmol applet. Since neutralization experiments are typically performed as one of the first steps in the characterization of an antibody to determine its breadth and potency, the NEP server can be used to predict antibody-epitope information at no additional experimental costs. NEP can be accessed on the internet at http://exon.niaid.nih.gov/nep.
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Registered trials
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