Table 1.

Commonly used data sets for DNA-binding site identification.

ID	Ref. No.	Notes
DB179	[33]	179 DNA-binding proteins, almost entirely nonredundant at 40% sequence identity
NB3797	[33]	3797 nonbinding proteins, significant redundancy at 35% sequence identity level (only 3482 independent clusters)
PD138	[27]	138 DNA-binding proteins, almost entirely nonredundant at 35% sequence identity, divided into seven structural classes
DISIS	[3]	78 DNA-binding proteins, close to nonredundant at 20% sequence identity
PDNA62	[34]	62 DNA-binding proteins, 78 chains, 57 nonredundant sequences at 30% identity.
NB110	[34]	110 nonbinding proteins, nonredundant at 30% sequence identity level, derived from the RS126 secondary structure data set by removing entries related to DNA
BIND54	[35]	Reported as 54 binding proteins, actually 58 chains, nonredundant at 30% sequence identity, original list of proteins was reported in [1]
NB250	[35]	250 nonbinding proteins, mostly nonredundant at a 35% sequence identity
DBP374	[18]	374 DNA-binding proteins, significant redundancy at a 25% sequence identity level
TS75	[18]	75 DNA-binding proteins, designed to be independent from DBP374 and PDNA62 but has some redundant entries in both at a 35% sequence identity level
PDNA-316	[29]	316 target proteins used in metaDBSite Web server, at 30% sequence identity
DNABindR171	[16]	171 proteins with mutual sequence identity ≤30% and each protein has at least 40 amino acid residues. All the structures have resolution better than 3.0 Å and an R factor less than 0.3