MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles

Guang Lan Zhang, David S. DeLuca, Derin B. Keskin, Lou Chitkushev, Tanya Zlateva, Ole Lund, Ellis L. Reinherz, Vladimir Brusic

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    MULTIPRED2 is a computational system for facile prediction of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR molecules. It enables prediction of peptide binding to products of individual HLA alleles, combination of alleles, or HLA supertypes. NetMHCpan and NetMHCIIpan are used as prediction engines. The 13 HLA Class I supertypes are A1, A2, A3, A24, B7, B8, B27, B44, B58, B62, C1, and C4. The 13 HLA Class II DR supertypes are DR1, DR3, DR4, DR6, DR7, DR8, DR9, DR11, DR12, DR13, DR14, DR15, and DR16. In total, MULTIPRED2 enables prediction of peptide binding to 1077 variants representing 26 HLA supertypes. MULTIPRED2 has visualization modules for mapping promiscuous T-cell epitopes as well as those regions of high target concentration – referred to as T-cell epitope hotspots. Novel graphic representations are employed to display the predicted binding peptides and immunological hotspots in an intuitive manner and also to provide a global view of results as heat maps. Another function of MULTIPRED2, which has direct relevance to vaccine design, is the calculation of population coverage. Currently it calculates population coverage in five major groups in North America. MULTIPRED2 is an important tool to complement wet-lab experimental methods for identification of T-cell epitopes. It is available at http://cvc.dfci.harvard.edu/multipred2/.
    Original languageEnglish
    JournalJournal of Immunological Methods
    Volume374
    Issue number1-2
    Pages (from-to)53-61
    ISSN0022-1759
    DOIs
    Publication statusPublished - 2011

    Keywords

    • Vaccine design
    • Human leukocyte antigen
    • HLA
    • T-cell epitope hotspots
    • HLA supertype
    • Promiscuous binding peptide

    Cite this

    Zhang, Guang Lan ; DeLuca, David S. ; Keskin, Derin B. ; Chitkushev, Lou ; Zlateva, Tanya ; Lund, Ole ; Reinherz, Ellis L. ; Brusic, Vladimir. / MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. In: Journal of Immunological Methods. 2011 ; Vol. 374, No. 1-2. pp. 53-61.
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    title = "MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles",
    abstract = "MULTIPRED2 is a computational system for facile prediction of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR molecules. It enables prediction of peptide binding to products of individual HLA alleles, combination of alleles, or HLA supertypes. NetMHCpan and NetMHCIIpan are used as prediction engines. The 13 HLA Class I supertypes are A1, A2, A3, A24, B7, B8, B27, B44, B58, B62, C1, and C4. The 13 HLA Class II DR supertypes are DR1, DR3, DR4, DR6, DR7, DR8, DR9, DR11, DR12, DR13, DR14, DR15, and DR16. In total, MULTIPRED2 enables prediction of peptide binding to 1077 variants representing 26 HLA supertypes. MULTIPRED2 has visualization modules for mapping promiscuous T-cell epitopes as well as those regions of high target concentration – referred to as T-cell epitope hotspots. Novel graphic representations are employed to display the predicted binding peptides and immunological hotspots in an intuitive manner and also to provide a global view of results as heat maps. Another function of MULTIPRED2, which has direct relevance to vaccine design, is the calculation of population coverage. Currently it calculates population coverage in five major groups in North America. MULTIPRED2 is an important tool to complement wet-lab experimental methods for identification of T-cell epitopes. It is available at http://cvc.dfci.harvard.edu/multipred2/.",
    keywords = "Vaccine design, Human leukocyte antigen, HLA, T-cell epitope hotspots, HLA supertype, Promiscuous binding peptide",
    author = "Zhang, {Guang Lan} and DeLuca, {David S.} and Keskin, {Derin B.} and Lou Chitkushev and Tanya Zlateva and Ole Lund and Reinherz, {Ellis L.} and Vladimir Brusic",
    year = "2011",
    doi = "10.1016/j.jim.2010.11.009",
    language = "English",
    volume = "374",
    pages = "53--61",
    journal = "Journal of Immunological Methods",
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    MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. / Zhang, Guang Lan; DeLuca, David S.; Keskin, Derin B.; Chitkushev, Lou; Zlateva, Tanya; Lund, Ole; Reinherz, Ellis L.; Brusic, Vladimir.

    In: Journal of Immunological Methods, Vol. 374, No. 1-2, 2011, p. 53-61.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles

    AU - Zhang, Guang Lan

    AU - DeLuca, David S.

    AU - Keskin, Derin B.

    AU - Chitkushev, Lou

    AU - Zlateva, Tanya

    AU - Lund, Ole

    AU - Reinherz, Ellis L.

    AU - Brusic, Vladimir

    PY - 2011

    Y1 - 2011

    N2 - MULTIPRED2 is a computational system for facile prediction of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR molecules. It enables prediction of peptide binding to products of individual HLA alleles, combination of alleles, or HLA supertypes. NetMHCpan and NetMHCIIpan are used as prediction engines. The 13 HLA Class I supertypes are A1, A2, A3, A24, B7, B8, B27, B44, B58, B62, C1, and C4. The 13 HLA Class II DR supertypes are DR1, DR3, DR4, DR6, DR7, DR8, DR9, DR11, DR12, DR13, DR14, DR15, and DR16. In total, MULTIPRED2 enables prediction of peptide binding to 1077 variants representing 26 HLA supertypes. MULTIPRED2 has visualization modules for mapping promiscuous T-cell epitopes as well as those regions of high target concentration – referred to as T-cell epitope hotspots. Novel graphic representations are employed to display the predicted binding peptides and immunological hotspots in an intuitive manner and also to provide a global view of results as heat maps. Another function of MULTIPRED2, which has direct relevance to vaccine design, is the calculation of population coverage. Currently it calculates population coverage in five major groups in North America. MULTIPRED2 is an important tool to complement wet-lab experimental methods for identification of T-cell epitopes. It is available at http://cvc.dfci.harvard.edu/multipred2/.

    AB - MULTIPRED2 is a computational system for facile prediction of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR molecules. It enables prediction of peptide binding to products of individual HLA alleles, combination of alleles, or HLA supertypes. NetMHCpan and NetMHCIIpan are used as prediction engines. The 13 HLA Class I supertypes are A1, A2, A3, A24, B7, B8, B27, B44, B58, B62, C1, and C4. The 13 HLA Class II DR supertypes are DR1, DR3, DR4, DR6, DR7, DR8, DR9, DR11, DR12, DR13, DR14, DR15, and DR16. In total, MULTIPRED2 enables prediction of peptide binding to 1077 variants representing 26 HLA supertypes. MULTIPRED2 has visualization modules for mapping promiscuous T-cell epitopes as well as those regions of high target concentration – referred to as T-cell epitope hotspots. Novel graphic representations are employed to display the predicted binding peptides and immunological hotspots in an intuitive manner and also to provide a global view of results as heat maps. Another function of MULTIPRED2, which has direct relevance to vaccine design, is the calculation of population coverage. Currently it calculates population coverage in five major groups in North America. MULTIPRED2 is an important tool to complement wet-lab experimental methods for identification of T-cell epitopes. It is available at http://cvc.dfci.harvard.edu/multipred2/.

    KW - Vaccine design

    KW - Human leukocyte antigen

    KW - HLA

    KW - T-cell epitope hotspots

    KW - HLA supertype

    KW - Promiscuous binding peptide

    U2 - 10.1016/j.jim.2010.11.009

    DO - 10.1016/j.jim.2010.11.009

    M3 - Journal article

    VL - 374

    SP - 53

    EP - 61

    JO - Journal of Immunological Methods

    JF - Journal of Immunological Methods

    SN - 0022-1759

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    ER -