The role of structural parameters in DNA cyclization

BMC Bioinformatics

Table 1 List of used sets of structural parameters

Parameter set name	Reference	Derivation approach	Number of nucleotides	Tilt	Roll	Twist	Shift	Slide	Rise
SET1	(Zhou et al., 2013) [43]	All-atom Monte Carlo simulations	Pentanucleotides	No	Yes	Yes	No	No	No
SET2	(Gabrielian and Pongor, 1996) [45]	Computationally combining SET3 and SET4	Trinucleotides	No	Yes	No	No	No	No
SET3	(Brukner et al., 1995) [44]	Endonuclease experiments	Trinucleotides	No	Yes	No	No	No	No
SET4	(Goodsell and Dickerson, 1994) [40]	Nucleosome positioning	Trinucleotides	No	Yes	No	No	No	No
SET5	(Ulyanov and James, 1995) [46]	NMR spectroscopy	Dinucleotides	Yes	Yes	Yes	Yes	Yes	Yes
SET6	(Rachofsky et al., 2001) [47]	Computational analysis of X-ray crystallography	Dinucleotides	Yes	Yes	Yes	Yes	Yes	Yes
SET7	(Olson et al., 1998) [48]	Computational analysis of X-ray crystallography	Dinucleotides	Yes	Yes	Yes	Yes	Yes	Yes

Reference information, derivation approach, and number of nucleotides are provided for each set of parameters. Additionally, the table denotes with “Yes” which of the six types of parameters is provided in the respective references. “No” is equivalent to using a default value for all nucleotide combinations. Default values: tilt = 0.00°; helix twist = 34.30°; shift = 0.00 Å; slide = 0.00 Å; rise = 3.40 Å. The exact values for each set of parameters are provided in Additional file 1: Tables S3 through S9 respectively for SET1 through SET7

ISSN: 1471-2105