Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins

Table 3 Identification of the native structure from decoys in PROSTAR decoy sets using different scoring functions^a

Parameters	Misfold	Ifu	Asilomar	Pdberr and sgpa
R_s ^b	24/24	22/43	41/41	5/5
R_p ^b	20/24	21/43	36/41	5/5
Atomic KBP^c	24/24	32/43	37/41	5/5
RAPDF^d	24/24	30/43	37/41	5/5
CDF^d	19/24	21/43	35/41	5/5
Residue contact potential^e	24/24	22/43	35/41	4/5

PROSTAR website [31].
^aThe first number of each column is the number of correctly identified decoys, and the second one after the slash is the total number of decoys. With either of the first two parameters the native structure is correctly identified if its value is smaller than that from any other structure in the decoy set. The results with the other parameters are taken from [14].
^bThe parameters developed in this study.
^cThe atomic Knowledge-Based Potential from Lu and Skolnick [14].
^dRAPDF and CDF are atomic and residue-based potentials, respectively, from Samudrala and Moult [13].
^eResidue-based quasichemical potential from Skolnick et al[33].

ISSN: 1472-6807