. Author manuscript; available in PMC: 2008 Oct 10.

Published in final edited form as: J Mol Biol. 2007 Jan 30;367(5):1511–1522. doi: 10.1016/j.jmb.2007.01.063

Table 2. Parameters chosen for each ProFunc method to classify hit “strength”.

	Code	“Strong” Hits	“Moderate” Hits	“Weak” Hits
Structure-based Methods
Secondary Structure Matching (SSM)	SSM	Zscore > 10	Zscore 6–10	Zscore <6
Templates (using internal scoring scheme)	ENZ, LIG, DNA, SIT	Confidence: “Certain” (E-value <1.00 x10⁻⁶) or “Probable” (E-value 1.00 x10⁻⁶ – 0.01)	Confidence: “Possible” (E-value 0.01 – 0.10)	Confidence: “Longshot” (E-value >0.10)

ENZ = Enzyme active site templates (CSA)

DNA = DNA based automatically generated templates

LIG = Ligand based automatically generated templates

SIT = “Reverse” template