Web-based design and evaluation of T-cell vaccine candidates.
Identifieur interne : 002107 ( PubMed/Corpus ); précédent : 002106; suivant : 002108Web-based design and evaluation of T-cell vaccine candidates.
Auteurs : James Thurmond ; Hyejin Yoon ; Carla Kuiken ; Karina Yusim ; Simon Perkins ; James Theiler ; Tanmoy Bhattacharya ; Bette Korber ; Will FischerSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2008.
English descriptors
- KwdEn :
- AIDS Vaccines (chemistry), Algorithms, Antigens (chemistry), Computers, Drug Design, Epitopes (chemistry), Epitopes, T-Lymphocyte (chemistry), HIV Infections (prevention & control), HIV Infections (virology), HIV-1 (genetics), HIV-1 (immunology), Humans, Internet, Software, T-Lymphocytes (metabolism), Technology, Pharmaceutical (instrumentation), Vaccines (chemistry).
- MESH :
- chemical , chemistry : AIDS Vaccines, Antigens, Epitopes, Epitopes, T-Lymphocyte, Vaccines.
- genetics : HIV-1.
- immunology : HIV-1.
- instrumentation : Technology, Pharmaceutical.
- metabolism : T-Lymphocytes.
- prevention & control : HIV Infections.
- virology : HIV Infections.
- Algorithms, Computers, Drug Design, Humans, Internet, Software.
Abstract
We present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential T-cell epitopes) as a metric. The vaccine design tool uses the recently published 'mosaic' method to generate protein sequences optimized for coverage of high-frequency k-mers; the coverage-assessment tools facilitate coverage comparisons for any potential antigens. To demonstrate these tools, we designed mosaic protein sets for B-clade HIV-1 Gag, Pol and Nef, and compared them to antigens used in a recent human vaccine trial.
DOI: 10.1093/bioinformatics/btn251
PubMed: 18515277
Links to Exploration step
pubmed:18515277Le document en format XML
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<affiliation><nlm:affiliation>Los Alamos National Laboratory, Los Alamos, NM 87545, USA.</nlm:affiliation>
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<author><name sortKey="Yoon, Hyejin" sort="Yoon, Hyejin" uniqKey="Yoon H" first="Hyejin" last="Yoon">Hyejin Yoon</name>
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<author><name sortKey="Kuiken, Carla" sort="Kuiken, Carla" uniqKey="Kuiken C" first="Carla" last="Kuiken">Carla Kuiken</name>
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<author><name sortKey="Yusim, Karina" sort="Yusim, Karina" uniqKey="Yusim K" first="Karina" last="Yusim">Karina Yusim</name>
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<author><name sortKey="Perkins, Simon" sort="Perkins, Simon" uniqKey="Perkins S" first="Simon" last="Perkins">Simon Perkins</name>
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<author><name sortKey="Theiler, James" sort="Theiler, James" uniqKey="Theiler J" first="James" last="Theiler">James Theiler</name>
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<author><name sortKey="Bhattacharya, Tanmoy" sort="Bhattacharya, Tanmoy" uniqKey="Bhattacharya T" first="Tanmoy" last="Bhattacharya">Tanmoy Bhattacharya</name>
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<author><name sortKey="Fischer, Will" sort="Fischer, Will" uniqKey="Fischer W" first="Will" last="Fischer">Will Fischer</name>
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<term>Epitopes (chemistry)</term>
<term>Epitopes, T-Lymphocyte (chemistry)</term>
<term>HIV Infections (prevention & control)</term>
<term>HIV Infections (virology)</term>
<term>HIV-1 (genetics)</term>
<term>HIV-1 (immunology)</term>
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<term>Internet</term>
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<term>T-Lymphocytes (metabolism)</term>
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<front><div type="abstract" xml:lang="en">We present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential T-cell epitopes) as a metric. The vaccine design tool uses the recently published 'mosaic' method to generate protein sequences optimized for coverage of high-frequency k-mers; the coverage-assessment tools facilitate coverage comparisons for any potential antigens. To demonstrate these tools, we designed mosaic protein sets for B-clade HIV-1 Gag, Pol and Nef, and compared them to antigens used in a recent human vaccine trial.</div>
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