Open Access Highly Accessed Research article

EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information

Thammakorn Saethang1*, Osamu Hirose2, Ingorn Kimkong3, Vu Anh Tran1, Xuan Tho Dang1, Lan Anh T Nguyen1, Tu Kien T Le1, Mamoru Kubo2, Yoichi Yamada2 and Kenji Satou2

Author Affiliations

1 Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan

2 Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan

3 Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand

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BMC Bioinformatics 2012, 13:313  doi:10.1186/1471-2105-13-313

Published: 24 November 2012

Additional files

Additional file 1:

Amino acid pairwise contact potentials (AAPPs) used in this study (http://www.genome.jp/aaindex/ webcite).

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Additional file 2:

Optimal subsets of AAPPs identified by EpicCapo+using 34 benchmark datasets.

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Additional file 3:

Features selected by EpicCapo+REF separated in each allele. The rank indicates importance of feature.

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Additional file 4:

Candidates of promiscuous epitopes identified from overlapping epitopes of influenza A viral strains: H1N1 (A/New York/4290/2009), H5N1 (A/Hong Kong/483/97), H1N1 (A/PR/8/34), and H3N2 (A/Aichi/2/68).

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Additional file 5:

Reference and added pMHC contact sites for HLA.

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Additional file 6:

The scaling of positional scoring matrices.

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Additional file 7:

The positional scoring matrix of EpicCapo used in the experiment that compared peptide-encoding schemes.

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