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. Author manuscript; available in PMC: 2008 Sep 11.
Published in final edited form as: J Chem Theory Comput. 2008;4(5):855–868. doi: 10.1021/ct800051k

Table 2.

Summary of the loop conformational predictions results with the standard and enhanced sampling procedures.

9-residue 13– residue
SGB/NP-X SGB/NP ddd AGB–γ AGBNP AGBNP+ AGBNP+
E 8 11(10) 19 6 4(3) 2 2
S 5(5) 7(14) 4(7) 4(7) 4(9) 5(10) 5(14)
M 2 3(4) 3 1 0 1 1(2)
E+S+M 15 21 26 11 8 8 8
〈RMSD〉 1.44 1.91 2.31 1.10 1.04 1.00 1.87
median RMSD 0.58 0.60 1.27 0.52 0.52 0.58 0.67

SGB/NP-X : SGB/NP with crystal symmetry

ddd : distance-dependent dielectric

E : number of energy errors (results listed for both enhanced and (standard) sampling)

S : number of sampling errors (results listed for both enhanced and (standard) sampling)

M : number of marginal errors (results listed for both enhanced and (standard) sampling)

The values listed were obtained with enhanced sampling; the values in parentheses were obtained with standard sampling.

〈RMSD〉 : average RMSD (in Å) of the lowest energy loops