Divide and Conquer Strategies for Protein Structure Prediction - Mathematical Approaches to Polymer Sequence Analysis and Related Problems - page 32

minOV.s 1 ;s 2 / is the length of actual overlap of s 1 and s 2 , i.e., the extent for

which both segments have residues in state i,

maxOV.s 1 ;s 2 / is the length of the total extent for which either of the segments
s 1 or s 2 has a residue in state i,
ı.s 1 ;s 2 / is equal to
min maxOV.s 1 ;s 2 / minOV.s 1 ;s 2 /; minOV.s 1 ;s 2 /;
int.len.s 1 /=2/; int.len.s 2 /=2/

The accuracy of prediction of the 13 servers currently monitored by EVAsec is
given in Table 2.1 . The second column of the table gives the number of proteins pre-
dicted by each method and the third column gives the average accuracy (Q 3 ) over all
proteins for the respective method. The results in Table 2.1 cannot be used for com-
parison, since different sets of proteins are used for each method. In Table 2.2 ,six
methods are compared on their largest common subset of 80 proteins. In Table 2.2 ,
also SOV and per-state accuracy measures C H ;C E ;C L are included.

Tabl e 2. 1 Average prediction accuracy (third column)
for each secondary structure server monitored in EVAsec
(data updated at April 2009). Different sets of proteins
are used for each method (the number of proteins used is
given in the second column)
Method Num. proteins Q 3

APSSP2 [ 39 ] 122 75.5

PHDpsi [ 37 ] 229 75.0

Porter [ 33 ] 73 80.0

PROF king [ 30 ] 230 72.1

PROFsec [ 40 ] 232 76.6

PSIpred [ 21 ] 224 77.9

SABLE [ 36 ] 232 76.1

SABLE2 [ 36 ] 159 76.8

SAM-T99sec [ 24 ] 204 77.3

SCRATCH (SSpro3) [ 34 ] 207 76.2

SSpro4 [ 34 ] 144 77.9

Ya s p i n [ 27 ] 157 73.6

Tabl e 2. 2 Performance comparison of six secondary structure prediction methods on their largest
common subset of 80 proteins as evaluated in EVAsec (data updated at April 2009). The average
of three different accuracy measures standard deviation are given: Q 3 (see ( 2.1 )), SOV (see

( 2.3 )) and C H ;C E ;C L (see ( 2.2 )). The first column of the table gives the rank of the corresponding
predictor
Rank

˙

Method Q 3 SOV C H C E C L

1 PROFsec 75.5 ˙ 1.4 74.9 ˙ 1.9 0.65 ˙ 0.03 0.70 ˙ 0.04 0.56 ˙ 0.02

PSIpred 76.8 ˙ 1.4 75.4 ˙ 2.0 0.67 ˙ 0.03 0.73 ˙ 0.04 0.55 ˙ 0.02

SAM-T99sec 77.2 ˙ 1.2 74.6 ˙ 1.5 0.67 ˙ 0.03 0.71 ˙ 0.03 0.59 ˙ 0.02

2 PHDpsi 73.4 ˙ 1.4 69.5 ˙ 1.9 0.64 ˙ 0.03 0.68 ˙ 0.04 0.52 ˙ 0.02

3 PROF king 71.6 ˙ 1.5 67.7 ˙ 2.0 0.62 ˙ 0.03 0.68 ˙ 0.04 0.51 ˙ 0.02