A structural alignment kernel for protein structures: Supplementary information

Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert and William Stafford Noble

Bioinformatics. 23(9):1090-1098, 2007.

Online supplement (PDF)

Sequence files are in fasta format. Structure files are tar files of PDB files. All remaining files are tab-delimited text, with identifiers in the first row and column.

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EC benchmark

• EC labels
• Sequences
• Structures
• MAMMOTH log E-values
• MAMMOTH kernel
• vectors
• vector kernel
• TOPS kernel
• torsion kernel
• contact kernel
• mismatch kernel
• sum kernel

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SCOP benchmark

• SCOP labels
• Sequences
• Structures
• MAMMOTH log E-values
• MAMMOTH kernel
• vectors
• vector kernel
• TOPS kernel
• torsion kernel
• contact kernel
• mismatch kernel
• sum kernel

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GO benchmark

• GO labels
• Sequences
• Structures
• MAMMOTH log E-values
• MAMMOTH kernel
• vectors
• vector kernel
• TOPS kernel
• torsion kernel
• contact kernel
• mismatch kernel
• sum kernel

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