. Author manuscript; available in PMC: 2018 Jun 13.

Published in final edited form as: J Chem Theory Comput. 2017 May 11;13(6):3049–3059. doi: 10.1021/acs.jctc.7b00254

Table 2.

Correlation between scores and RMSD in decoy set 1.

	Correlation with RMSD₁			Correlation with RMSD₂
Scoring function	Full protocol	w/o optimization of membrane orientation	w/o MD	Full protocol	w/o optimization of membrane orientation	w/o MD
IMM1	0.28 (0.1)	0.35 (0.1)	0.24 (0.1)	0.38 (0.1)	0.35 (0.1)	0.31 (0.1)
IMM1-p36	0.29 (0.2)	0.35 (0.1)	0.24 (0.2)	0.40 (0.1)	0.35 (0.1)	0.34 (0.1)
GBSW	0.26 (0.2)	0.32 (0.1)	0.22 (0.2)	0.36 (0.2)	0.32 (0.1)	0.32 (0.2)
HDGBv2	0.23 (0.2)	0.26 (0.1)	0.16 (0.2)	0.31 (0.2)	0.26 (0.1)	0.23 (0.1)
HDGBv3	0.23 (0.2)	0.26 (0.1)	0.17 (0.2)	0.32 (0.2)	0.26 (0.1)	0.25 (0.2)
HDGBvdW	0.15 (0.2)	0.23 (0.1)	0.12 (0.1)	0.24 (0.2)	0.23 (0.1)	0.19 (0.1)
DFIRE	0.35 (0.2)	0.37 (0.2)	0.36 (0.2)	0.38 (0.2)	0.37 (0.2)	0.39 (0.2)

Average Spearman’s rank correlation coefficients between scores and RMSD1 (without consideration of different orientations) and RMSD2 (considering different orientations) for a membrane width of 28.5 Å (not applicable for DFIRE). Results are compared between scores calculated for the full protocol, without optimization of the membrane orientation, and without the MD step. Values given in parentheses indicate standard deviations with respect to variations between different proteins.