{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T13:04:53Z","timestamp":1765544693140,"version":"3.37.3"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,14]],"date-time":"2019-02-14T00:00:00Z","timestamp":1550102400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI131722"],"award-info":[{"award-number":["R01 AI131722"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Vanderbilt Program for Next Generation Vaccines"},{"name":"Vanderbilt Molecular Biophysics Training Program","award":["T32GM008320"],"award-info":[{"award-number":["T32GM008320"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A better understanding of antibody responses to HIV-1 infection in humans can provide novel insights for the development of an effective HIV-1 vaccine. Neutralization fingerprinting (NFP) is an efficient and accurate algorithm for delineating the epitope specificities found in polyclonal antibody responses to HIV-1 infection. Here, we report the development of NFPws, a web server implementation of the NFP algorithm. The server takes as input serum neutralization data for a set of diverse viral strains, and uses a mathematical model to identify similarities between the serum neutralization pattern and the patterns for known broadly neutralizing monoclonal antibodies (bNAbs), in order to predict the prevalence of bNAb epitope specificities in the given serum. In addition, NFPws also computes and displays a number of estimates related to prediction confidence, as well as the likelihood of presence of novel, previously uncharacterized, antibody specificities in a given serum. NFPws also implements a JSmol viewer for molecular structure visualization of the prediction results. Overall, the NFPws server will be an important tool for the identification and analysis of epitope specificities of bNAb responses against HIV-1.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>NFPws is freely available to access at (http:\/\/iglab.accre.vanderbilt.edu\/NFPws). The webserver is developed using html, CSS, javascript and perl CGI scripts. The NFP algorithm is implemented with scripts written in octave, linux shell and perl. JSmol is implemented to visualize the prediction results on a representative 3D structure of an HIV-1 antigen.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz097","type":"journal-article","created":{"date-parts":[[2019,2,14]],"date-time":"2019-02-14T13:00:24Z","timestamp":1550149224000},"page":"3502-3504","source":"Crossref","is-referenced-by-count":7,"title":["NFPws: a web server for delineating broadly neutralizing antibody specificities from serum HIV-1 neutralization data"],"prefix":"10.1093","volume":"35","author":[{"given":"Nagarajan","family":"Raju","sequence":"first","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN, USA"},{"name":"Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center , Nashville, TN, USA"}]},{"given":"Ian","family":"Setliff","sequence":"additional","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN, USA"},{"name":"Program in Chemical & Physical Biology, Vanderbilt University Medical Center , Nashville, TN, USA"}]},{"given":"Ivelin S","family":"Georgiev","sequence":"additional","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN, USA"},{"name":"Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center , Nashville, TN, USA"},{"name":"Department of Electrical Engineering and Computer Science, Vanderbilt University , Nashville, TN, USA"},{"name":"Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center , Nashville, TN, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,2,14]]},"reference":[{"key":"2023013108052669400_btz097-B1","doi-asserted-by":"crossref","first-page":"4688","DOI":"10.1128\/JVI.07163-11","article-title":"Two distinct broadly neutralizing antibody specificities of different clonal lineages in a single HIV-1-infected donor: implications for vaccine design","volume":"86","author":"Bonsignori","year":"2012","journal-title":"J. Virol"},{"key":"2023013108052669400_btz097-B2","doi-asserted-by":"crossref","first-page":"e1006148.","DOI":"10.1371\/journal.ppat.1006148","article-title":"Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting","volume":"13","author":"Doria-Rose","year":"2017","journal-title":"PLoS Pathog"},{"key":"2023013108052669400_btz097-B3","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1016\/j.cell.2015.06.003","article-title":"Immunization for HIV-1 broadly neutralizing antibodies in human ig knockin mice","volume":"161","author":"Dosenovic","year":"2015","journal-title":"Cell"},{"key":"2023013108052669400_btz097-B4","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1097\/COH.0b013e328363a90e","article-title":"Elicitation of HIV-1-neutralizing antibodies against the CD4-binding site","volume":"8","author":"Georgiev","year":"2013","journal-title":"Curr. Opin. HIV AIDS"},{"key":"2023013108052669400_btz097-B5","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1126\/science.1233989","article-title":"Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization","volume":"340","author":"Georgiev","year":"2013","journal-title":"Science"},{"key":"2023013108052669400_btz097-B6","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/nature13601","article-title":"Broad and potent neutralization of HIV-1 by a human antibody that recognizes an intersubunit site on the envelope glycoprotein","volume":"515","author":"Huang","year":"2014","journal-title":"Nature"},{"key":"2023013108052669400_btz097-B7","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1126\/science.aac5894","article-title":"Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen","volume":"349","author":"Jardine","year":"2015","journal-title":"Science"},{"key":"2023013108052669400_btz097-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1743-422X-10-347","article-title":"Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models","volume":"10","author":"Lacerda","year":"2013","journal-title":"Virol. J"},{"key":"2023013108052669400_btz097-B9","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nature13808","article-title":"Structure and immune recognition of trimeric pre-fusion HIV-1 Env","volume":"514","author":"Pancera","year":"2014","journal-title":"Nature"},{"key":"2023013108052669400_btz097-B10","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/j.cell.2016.04.010","article-title":"Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G","volume":"165","author":"Stewart-Jones","year":"2016","journal-title":"Cell"},{"key":"2023013108052669400_btz097-B11","doi-asserted-by":"crossref","first-page":"e1001028.","DOI":"10.1371\/journal.ppat.1001028","article-title":"A limited number of antibody specificities mediate broad and potent serum neutralization in selected HIV-1 infected individuals","volume":"6","author":"Walker","year":"2010","journal-title":"PLoS Pathog"},{"key":"2023013108052669400_btz097-B12","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.tibs.2014.12.006","article-title":"Insights into the trimeric HIV-1 envelope glycoprotein structure","volume":"40","author":"Ward","year":"2015","journal-title":"Trends Biochem. Sci"},{"key":"2023013108052669400_btz097-B13","doi-asserted-by":"crossref","first-page":"10598","DOI":"10.1073\/pnas.1309215110","article-title":"Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues","volume":"110","author":"West","year":"2013","journal-title":"Proc. Natl. Acad. Sci. 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