Improved methods for predicting peptide binding affinity to MHC class II molecules

TY - JOUR

T1 - Improved methods for predicting peptide binding affinity to MHC class II molecules

AU - Jensen, Kamilla Kjærgaard

AU - Andreatta, Massimo

AU - Marcatili, Paolo

AU - Buus, Søren

AU - Greenbaum, Jason A.

AU - Yan, Zhen

AU - Sette, Alessandro

AU - Peters, Bjoern

AU - Nielsen, Morten

PY - 2018/7

Y1 - 2018/7

N2 - Major histocompatibility complex class II (MHC-II) molecules are expressed on the surface of professional antigen-presenting cells where they display peptides to T helper cells, which orchestrate the onset and outcome of many host immune responses. Understanding which peptides will be presented by the MHC-II molecule is therefore important for understanding the activation of T helper cells and can be used to identify T-cell epitopes. We here present updated versions of two MHC-II-peptide binding affinity prediction methods, NetMHCII and NetMHCIIpan. These were constructed using an extended data set of quantitative MHC-peptide binding affinity data obtained from the Immune Epitope Database covering HLA-DR, HLA-DQ, HLA-DP and H-2 mouse molecules. We show that training with this extended data set improved the performance for peptide binding predictions for both methods. Both methods are publicly available at www.cbs.dtu.dk/services/NetMHCII-2.3 and www.cbs.dtu.dk/services/NetMHCIIpan-3.2.

AB - Major histocompatibility complex class II (MHC-II) molecules are expressed on the surface of professional antigen-presenting cells where they display peptides to T helper cells, which orchestrate the onset and outcome of many host immune responses. Understanding which peptides will be presented by the MHC-II molecule is therefore important for understanding the activation of T helper cells and can be used to identify T-cell epitopes. We here present updated versions of two MHC-II-peptide binding affinity prediction methods, NetMHCII and NetMHCIIpan. These were constructed using an extended data set of quantitative MHC-peptide binding affinity data obtained from the Immune Epitope Database covering HLA-DR, HLA-DQ, HLA-DP and H-2 mouse molecules. We show that training with this extended data set improved the performance for peptide binding predictions for both methods. Both methods are publicly available at www.cbs.dtu.dk/services/NetMHCII-2.3 and www.cbs.dtu.dk/services/NetMHCIIpan-3.2.

KW - Affinity predictions

KW - Immunogenic peptides

KW - MHC binding specificity

KW - Peptide-MHC binding

KW - T-cell epitope

U2 - 10.1111/imm.12889

DO - 10.1111/imm.12889

M3 - Journal article

C2 - 29315598

AN - SCOPUS:85041595230

SN - 0019-2805

VL - 154

SP - 394

EP - 406

JO - Immunology

JF - Immunology

IS - 3

ER -