Program/Server | Mainly-α 19 str.a | Mainly-β 19 str.a | Mixed-α-β 15 str.a | Average performance (%) |
---|
CE | 17 | 19 | 13 | 93 |
DALI | 14 | 19 | 14 | 89 |
DEJAVU | 14 | 19 | 9 | 79 |
GANGSTA
|
18
b
|
19
|
15
|
98
|
LOCK | 0 | 14 | 11 | 47 |
MATRAS | 11 | 19 | 14 | 83 |
SSM | 5 | 13 | 10 | 53 |
TOP | 14 | 18 | 12 | 83 |
TOPS | 2 | 15 | 14 | 59 |
TOPSCAN | 15 | 12 | 9 | 68 |
VAST | 12 | 17 | 15 | 83 |
YAKUSA | 17 | 19 | 14 | 94 |
- Except for GANGSTA all data were taken from literature [52, 53]. Average performances differ slightly, since structures with low secondary structure content were omitted. The 53 proteins of the Novotny dataset (see method section) were aligned against the SCOP40 reference database. For the GANGSTA evaluation the assignment of a reference structure was successful, if at least one target with appropriate CATH topology was found among the top 100 ranked protein domains.
- a Target protein structures belonging to the specified CATH class that are used for assignment to the appropriate CATH topology (for details see text).
- b Since protein 1c3u was moved to another topology class in more recent CATH versions, 18 is the maximum number of correct structure alignments achievable. Thus, preventing GANGSTA from reaching the maximum performance of 100% (Table S5 [see Additional file 1]).