An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles

Shen, Wen-Jun; Zhang, Shaohong; Wong, Hau-San

doi:10.1186/1477-5956-11-S1-S15

Proteome Science

Table 7 Comparison of OWA-PSSM with four pan-specific methods in identifying MHC II-peptide binding cores.

From: An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles

PDB ID	OWA-PSSM	TEPITOPE	TEPITOPEpan	MultiRTA	NetMHCIIpan-2.0
4E41	IGILNAAKV	IGILNAAKV	IGILNAAKV	IGILNAAKV	LIGILNAAK
1A6A	MRMATPLLM	MRMATPLLM	MRMATPLLM	MRMATPLLM	MRMATPLLM
1AQD	WRFLRGYHQ	WRFLRGYHQ	WRFLRGYHQ	WRFLRGYHQ	WRFLRGYHQ
1BX2	VHFFKNIVT	VHFFKNIVT	VHFFKNIVT	VHFFKNIVT	VVHFFKNIV
1DLH	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1FV1	FKNIVTPRT	FKNIVTPRT	FKNIVTPRT	VHFFKNIVT	FFKNIVTPR
1FYT	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1H15	YHFVKKHVH	YHFVKKHVH	YHFVKKHVH	YHFVKKHVH	YHFVKKHVH
1HQR	FKNIVTPRT	FKNIVTPRT	FKNIVTPRT	VHFFKNIVT	FFKNIVTPR
1HXY	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1J8H	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1JWM	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1JWS	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1JWU	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1KG0	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1KLG	IGILNAAKV	IGILNAAKV	IGILNAAKV	IGILNAAKV	LIGILNAAK
1KLU	IGTLNAAKV	IGTLNAAKV	IGTLNAAKV	IGTLNAAKV	IGTLNAAKV
1LO5	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1PYW	FVKQNAAAL	FVKQNAAAL	FVKQNAAAL	FVKQNAAAL	FVKQNAAAL
1R5I	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
1SJE	VIPMFSALS	VIPMFSALS	VIPMFSALS	VIPMFSALS	VIPMFSALS
1SJH	VIPMFSALS	VIPMFSALS	VIPMFSALS	VIPMFSALS	VIPMFSALS
1T5W	YSDQATPLL	YSDQATPLL	YSDQATPLL	SDQATPLLL	YSDQATPLL
1T5X	YSDQATPLL	YSDQATPLL	YSDQATPLL	SDQATPLLL	YSDQATPLL
1YMM	VHFFKNIVT	VHFFKNIVT	VHFFKNIVT	VHFFKNIVT	VHFFKNIVT
1ZGL	FKNIVTPRT	FKNIVTPRT	FKNIVTPRT	VHFFKNIVT	FFKNIVTPR
2FSE	FKGEQGPKG	FKGEQGPKG	FKGEQGPKG	FKGEQGPKG	FKGEQGPKG
2G9H	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
2IAM	IGILNAAKV	IGILNAAKV	IGILNAAKV	IGILNAAKV	LIGILNAAK
2IAN	IGTLNAAKV	IGTLNAAKV	IGTLNAAKV	IGTLNAAKV	IGTLNAAKV
2ICW	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
2IPK	WVKQNTLKL	WVKQNTLKL	WVKQNTLKL	WVKQNTLKL	WVKQNTLKL
2OJE	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
2Q6W	WRSDEALPL	-	WRSDEALPL	WRSDEALPL	WRSDEALPL
2SEB	MRADAAAGG	MRADAAAGG	YMRADAAAG	MRADAAAGG	YMRADAAAG
3C5J	IILNHPGQI	-	VIILNHPGQ	IILNHPGQI	IILNHPGQI
3L6F	YEKLSAEQS	YEKLSAEQS	YEKLSAEQS	YEKLSAEQS	YEKLSAEQS
3PDO	MRMATPLLM	MRMATPLLM	MRMATPLLM	MRMATPLLM	MRMATPLLM
3PGD	MRMATPLLM	MRMATPLLM	MRMATPLLM	MRMATPLLM	KMRMATPLL
3S4S	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
3S5L	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL	YVKQNTLKL
Correct	41/41		39/41	36/41	32/41
Correct I	39/39	39/39	38/39	34/39	30/39
Correct II	2/2		1/2	2/2	2/2

Incorrectly predicted binding cores are highlighted in bold. "Correct" gives the number of correctly identified cores over 41 X-ray structures. "Correct I" gives the number of correctly identified cores over 39 X-ray structures whose DRB alleles are predictable by TEPITOPE. "Correct II" gives the number of correctly identified cores over 2 X-ray structures whose DRB alleles are not predictable by TEPITOPE. The PSSMs of TEPITOPE, TEPITOPEpan and the results of MultiRTA, NetMHCIIpan-2.0 were obtained from their respective web servers.

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ISSN: 1477-5956

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