Table 3

Identification of the native structure from decoys in PROSTAR decoy sets using different scoring functionsa

Parameters

Misfold

Ifu

Asilomar

Pdberr and sgpa


Rs b

24/24

22/43

41/41

5/5

Rp b

20/24

21/43

36/41

5/5

Atomic KBPc

24/24

32/43

37/41

5/5

RAPDFd

24/24

30/43

37/41

5/5

CDFd

19/24

21/43

35/41

5/5

Residue contact potentiale

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].

Bahadur and Chakrabarti BMC Structural Biology 2009 9:76   doi:10.1186/1472-6807-9-76

Open Data