. Author manuscript; available in PMC: 2016 Aug 11.

Published in final edited form as: J Chem Theory Comput. 2015 Aug 11;11(8):3714–3728. doi: 10.1021/acs.jctc.5b00271

Table 4.

abs_rmsd, rel_rmsd for type I and II test sets. In the case of the protein/DNA complex with the original GB-neck parameters, we show two cases: 1) the original GB-neck parameters were applied to both protein and DNA. 2) The original GB-neck parameters applied to DNA while GB-neck2 parameters were applied to protein (results shown in parentheses).

	Test set name	GB-neck		GB-neck2		%reduced_error
	Test set name	abs_rmsd	rel_rmsd	abs_rmsd	rel_rmsd	abs_rmsd	rel_rmsd
Type I	dnadup_plus150	70.8	26.2	16.4	10.7	77%	59%
Type I	rnadup_plus200	144.3	11.1	21.5	10.4	85%	6%
Type II	DNA duplex (CGCGAATTCGCG)2	104.2	17.8	15.3	13.6	85%	24%
	RNA duplex (CGCGAAUUCGCG)2	177.4	13.3	29.9	9.9	83%	26%
	Protein/DNA complex 1GCC	126.0 (63.7)	23.3 (46.9)	39.2	19.1	69% (38%)	18% (59%)