Table 2

Identification of peptide binding cores.

Allele

Peptide

Core

TEPITOPE

SMM-align

NetMHCIIPan

NN-W-P1

NN-W


DRB1*0101

AGFKGEQGPKGEPG

FKGEQGPKG

FKGEQGPKG

FKGEQGPKG

FKGEQGPKG

FKGEQGPKG

FKGEQGPKG

DRB1*0101

GELIGILNAAKVPAD

IGILNAAKV

IGILNAAKV

IGILNAAKV

IGILNAAKV

IGILNAAKV

IGILNAAKV

DRB1*0101

PEVIPMFSALSEGATP

VIPMFSALS

VIPMFSALS

VIPMFSALS

VIPMFSALS

VIPMFSALS

VIPMFSALS

DRB1*0101

PKYVKQNTLKLAT

YVKQNTLKL

YVKQNTLKL

YVKQNTLKL

YVKQNTLKL

YVKQNTLKL

YVKQNTLKL

DRB1*0101

VGSDWRFLRGYHQYA

WRFLRGYHQ

WRFLRGYHQ

WRFLRGYHQ

WRFLRGYHQ

WRFLRGYHQ

WRFLRGYHQ

DRB1*0101

AFVKQNAAALA

FVKQNAAAL

FVKQNAAAL

    VKQNAAALA

FVKQNAAAL

FVKQNAAAL

FVKQNAAAL

DRB1*0101

AAYSDQATPLLLSPR

YSDQATPLL

YSDQATPLL

YSDQATPLL

YSDQATPLL

YSDQATPLL

YSDQATPLL

DRB1*0301

PVSKMRMATPLLMQA

MRMATPLLM

MRMATPLLM

MRMATPLLM

MRMATPLLM

MRMATPLLM

    VSKMRMATP

DRB1*0401

AYMRADAAAGGA

MRADAAAGG

MRADAAAGG

MRADAAAGG

    YMRADAAAG

    YMRADAAAG

    AYMRADAAA

DRB1*0401

PKYVKQNTLKLAT

YVKQNTLKL

YVKQNTLKL

YVKQNTLKL

YVKQNTLKL

YVKQNTLKL

    KYVKQNTLK

DRB1*1501

ENPVVHFFKNIVTPR

VHFFKNIVT

VHFFKNIVT

VHFFKNIVT

VHFFKNIVT

VHFFKNIVT

    VVHFFKNIV

DRB1*1501

ENPVVHFFKNIVTPRGGSGGGGG

VHFFKNIVT

VHFFKNIVT

VHFFKNIVT

VHFFKNIVT

VHFFKNIVT

    VVHFFKNIV

DRB5*0101

GGVYHFVKKHVHES

YHFVKKHVH

YHFVKKHVH

YHFVKKHVH

YHFVKKHVH

YHFVKKHVH

YHFVKKHVH

DRB5*0101

NPVVHFFKNIVTPRTPPPSQ

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT

DRB5*0101

VHFFKNIVTPRTPGG

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT

FKNIVTPRT


Correct

15/15

14/15

14/15

14/15

10/15


15 HLA-DR restricted peptides compiled from the protein database [32]. The columns in the table state the HLA restriction, the peptide sequence, the binding core as determined from the protein structure, followed by the binding core as predicted by TEPITOPE, SMM-align, NetMHCIIpan, NN-W-P1 (the NN-based method including data redundancy step-size rescaling and P1-PSSM encoding), and NN-W (the NN-based method including data redundancy step-size rescaling), respectively. Erroneous predictions are underlined.

Nielsen and Lund BMC Bioinformatics 2009 10:296   doi:10.1186/1471-2105-10-296

Open Data