Discovering co-occurring patterns and their biological significance in protein families

BMC Bioinformatics

Table 1 Results from the nine protein families.

Protein name	Pfam ID	Co-occurrence cluster count	Size of the best cluster	PDB ID of the best cluster	Average APC distance of the best cluster	Average pairwise distance
Lipocalin	PF00061	6	4	2CZT	16.77 Å	19.26 Å
Bacterial rhodopsins	PF01036	2	2	1JGJ	16.52 Å	22.51 Å
Bacterial antenna complex	PF00556	4	5	1IJD	0 Å	19.92 Å
Cytochrome c oxidase subunit I	PF00115	2	25	3OM3	26.78 Å*	30.00 Å
Photosynthetic reaction centre protein family	PF00124	2	7	1PSS	27.87 Å	30.19 Å
Leptin	PF02024	2	14	1AX8	15.73 Å	18.37 Å
G-alpha subunit	PF00503	3	8	4G5O	15.78 Å	27.45 Å
Protein kinase domain	PF00069	2	2	3OZ6	15.32 Å	27.51 Å
Tyrosine kinase	PF07714	2	8	4HW7	14.43 Å	24.99 Å

Displays the Co-occurrence Cluster with the lowest average eigenvector distance, and are used to verify the algorithm's effectiveness with a PDB structure. The shorter distance in the comparison is bolded. * means that one or more APCs were not found.

ISSN: 1471-2105