Research article
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information
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
BMC Bioinformatics 2012, 13:313 doi:10.1186/1471-2105-13-313
Published: 24 November 2012Additional 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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