Prediction of β-barrel membrane proteins by searching for restricted domains

BMC Bioinformatics

Table 1 Summary of the parameters for β-barrel prediction

score^a	definition of the parameter^b	value used^c
EBSS	β-strand length	10 aa
	Core region	4 aa
BSN^d	Number of individual peaks	EBSS >2.0
	β-strand length	10 aa
HPS	β-strand length	10 aa
	Loop length	0–14 aa^d
BBS	HPS cut off	>6.0
BBS275^d	HPS cut off	>6.0
	Sliding window	275 aa
BSHS225^d	EBSS cut off for strands	>2.0
	Sliding window	225 aa

For detailed descriptions see text. ^a ... The different intermediate scores necessary for final calculation of the β-barrel score; ^b ... the scores are calculated by various physicochemical assumptions; ^c ... the parameters for the different scores were used as suggested by Wimley, if not stated differently [14]; ^d ... described in here

ISSN: 1471-2105