Skip to main content
. 2011 Mar 18;67(Pt 4):303–312. doi: 10.1107/S0907444910051218

Table 2. Protocols used in benchmark calculations.

For main-chain deletion, only the identity scoring matrix was employed. ‘Variable’ thresholds were calculated from the respective sequence alignment. Protocol 1 corresponds to the algorithm published by Schwarzenbacher et al. (2004).

Protocol Main-chain window Threshold Side-chain matrix Window Threshold B factor
1 0 0.0 Identity 0 1.0 Original
2 3 0.2 Identity 0 1.0 Original
3 5 Variable Identity 0 1.0 Original
4 0 0.0 BLOSUM62 1 0.2 Original
5 5 Variable BLOSUM62 1 0.2 Original
6 0 0.0 Identity 0 1.0 Sequence-similarity based (matrix = BLOSUM62, window = 5, factor = 80)
7 5 Variable Identity 0 1.0 Sequence-similarity based (matrix = BLOSUM62, window = 5, factor = 80)
8 0 0.0 Identity 0 1.0 Accessible surface area-based (factor = 12)
9 5 Variable Identity 0 1.0 Accessible surface area-based (factor = 12)
10 0 0.0 Identity 0 1.0 Sequence-similarity based (matrix = BLOSUM62, window = 5, factor = 60) + accessible surface area-based (factor = 8)
11 5 Variable Identity 0 1.0 Sequence-similarity based (matrix = BLOSUM62, window = 5, factor = 60) + accessible surface area-based (factor = 8)
12 5 Variable BLOSUM62 1 0.2 Sequence-similarity based (matrix = BLOSUM62, window = 5, factor = 60) + accessible surface area-based (factor = 8)