Kringle domain
Few SSE example
Basic info about members of the topology level:
|
|
Resolution () |
length |
SSE content (%) |
|
1b2i |
20 models |
83 |
13,6 |
|
1ceaA |
2,1 |
80 |
11 |
|
1kdu |
1 model |
85 |
18 |
|
1kiv |
2,1 |
78 |
7,7 |
|
1krn |
1,67 |
79 |
12,7 |
|
1pk4 |
1,9 |
79 |
12,7 |
|
1pmlA |
2,38 |
86 |
22 |
|
5hpgA |
1,66 |
84 |
7,1 |
1b2i used model number 1.
ServersÕ results:
Number in parentheses in columnÓ Another true positivesÓ means number of
retrieved true positives
First columns of the tables contain PDB ID of structures.
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
yes |
yes |
4 |
50 min |
|
1cea |
Yes |
Yes |
4. |
7min |
|
1kdu |
Yes |
Yes |
4. |
6min |
|
1kiv |
Yes |
Yes |
4. |
4min |
|
1krn |
Yes |
Yes |
4 |
5min |
|
1pk4 |
Yes |
Yes |
4 |
6min |
|
1pml |
yes |
yes |
4 |
6min |
|
5hpg |
yes |
Yes |
4 |
6min |
Dali
has all these structures under 5hpgA, therefore are the results the same, Dali
doesnÕt accept PDB with negative numbers for atoms
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
no |
Yes (5) |
2 |
Sec |
|
1cea |
No (3.) |
Yes |
2 |
Sec |
|
1kdu |
No |
no |
1 |
Sec |
|
1kiv |
No (5.) |
Yes |
1 |
Sec |
|
1krn |
No (11.) |
Yes |
2 |
Sec |
|
1pk4 |
No (9) |
Yes |
2 |
Sec |
|
1pml |
No (6) |
Yes |
1 |
Sec |
|
5hpg |
Yes |
Yes |
2 |
Sec |
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
No |
Yes(2) |
2 |
7min |
|
1cea |
No |
Yes(1) |
2 |
47 |
|
1kdu |
Yes |
No |
2 |
60 |
|
1kiv |
Yes |
Yes(3) |
3 |
40 |
|
1krn |
Yes |
Yes(3) |
3 |
37 |
|
1pk4 |
No |
Yes(4) |
3 |
45 |
|
1pml |
No |
Yes(4) |
4 |
37 |
|
5hpg |
yes |
Yes (3) |
2 |
35 |
I
searched only first fifty results or so.
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
no |
no |
1 |
2 min |
|
1cea |
No (3.) |
Yes (1-2) |
1 |
2min |
|
1kdu |
No (5.) |
Yes (1-2) |
1 |
2min |
|
1kiv |
No |
Yes (1-3) |
1 |
2min |
|
1krn |
Yes |
Yes (2) |
3 |
2min |
|
1pk4 |
No (2.) |
Yes (2) |
3 |
2min |
|
1pml |
No (4.) |
Yes (3) |
1 |
2min |
|
5hpg |
No (15.) |
Yes (2) |
1 |
2min |
Some of the
true positives were very far away.
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
No |
Yes(1) |
2 |
6 min |
|
1cea |
No |
Yes(1) |
2 |
8 min |
|
1kdu |
No |
Yes(2) |
3 |
12 min |
|
1kiv |
No |
Yes(1) |
1 |
8 min |
|
1krn |
No |
Yes(1) |
2 |
6 min |
|
1pk4 |
Yes |
Yes(1) |
2 |
8 min |
|
1pml |
No |
Yes (1) |
2 |
8 min |
|
5hpg |
no |
Yes (1) |
2 |
8 min |
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
no |
Yes (3) |
1 |
5min |
|
1cea |
No hits |
|
|
5min |
|
1kdu |
no |
Yes (6) |
1 |
11 min |
|
1kiv |
No |
Yes (7) |
6 |
7 min |
|
1krn |
No |
Yes (8) |
6. |
6 min |
|
1pk4 |
No (4.) |
Yes (6) |
6 |
4min |
|
1pml |
No |
Yes (6) |
7 |
4min |
|
5hpg |
yes |
Yes (6) |
6 |
5min |
If Vast donÕt
found at least two SSE than it doesnÕt continue in search.
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
Yes |
Yes(7) |
9 |
|
|
1cea |
Yes |
Yes(36) |
No |
|
|
1kdu |
Yes |
Yes(36) |
No |
|
|
1kiv |
Yes |
Yes(36) |
No |
|
|
1krn |
Yes |
Yes(36) |
No |
|
|
1pk4 |
Yes |
Yes(36) |
No |
|
|
1pml |
Yes |
Yes(36) |
No |
|
|
5hpg |
yes |
Yes(36) |
no |
|
Against whole
pdb database, without time, because I used pre-computed results(more in paper).
Big numbers of true positive due to redundancy in PDB
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
DoesnÕt work |
|
|
|
|
1cea |
yes |
Yes(7) |
9 |
113 min |
|
1kdu |
no |
no |
1 |
81 min |
|
1kiv |
DoesnÕt work |
|
|
|
|
1krn |
yes |
Yes(7) |
9 |
113 min |
|
1pk4 |
Yes |
Yes (7) |
9 |
112 min |
|
1pml |
no |
no |
1 |
136 min |
|
5hpg |
yes |
Yes(2) |
3 |
101 min |
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
no |
Yes (3-5) |
3(5) |
4 min |
|
1cea |
No |
Yes (3-5) |
3(5) |
3 min |
|
1kdu |
No |
Yes (3-5) |
3(5) |
4 min |
|
1kiv |
No |
Yes (3-5) |
4(6) |
4 min |
|
1krn |
No |
Yes (3-5) |
3(5) |
5 min |
|
1pk4 |
No |
Yes (3-5) |
4(6) |
7 min |
|
1pml |
No |
Yes (3-5) |
4(6) |
6 min |
|
5hpg |
no |
Yes (3-5) |
4(6) |
9 min |
40% replist of
current PDB
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
DoesnÕt work |
|
|
|
|
1cea |
Yes |
Yes(1) |
3 |
Sec |
|
1kdu |
Yes |
Yes(4) |
3 |
Sec |
|
1kiv |
Yes |
No |
2 |
Sec |
|
1krn |
Yes |
No |
2 |
Sec |
|
1pk4 |
No |
Yes (1) |
2 |
Sec |
|
1pml |
No |
Yes(4) |
4 |
Sec |
|
5hpg |
No |
Yes(1) |
2 |
Sec |
1b2i doesnÕt provide any results, because program can not detect enough SSE.
Pride
|
|
Found itself on first position |
Another true positive |
Position of first false positive |
Time |
|
1b2i |
Yes |
No |
2 |
Sec |
|
1cea |
Yes |
Yes(1) |
3 |
Sec |
|
1kdu |
No |
no |
1 |
Sec |
|
1kiv |
No |
yes |
1 |
Sec |
|
1krn |
No |
no |
1 |
Sec |
|
1pk4 |
No |
no |
1 |
Sec |
|
1pml |
No |
no |
1 |
Sec |
|
5hpg |
Yes |
Yes (4) |
6. |
Sec |
First non-trivial solution for 1krn, 1pk4, 1pml were found at position 34.,37 and 59., respectively. Therefore we took them as the serverÕs failure.
|
Server |
Trivial solution found (itself) |
Non-trivial solutions found |
Rank of first false positive |
Time |
|
CE |
8 |
8 |
9 |
|
|
Dali |
8 |
8 |
2 |
5-50 |
|
Dejavu |
4 |
4 |
1-9 |
80-135 |
|
Lock |
1 |
8 |
1-3 |
5-10 |
|
Matras |
0 |
8 |
3-4 |
3-10 |
|
Pride |
3 |
3 |
1-6 |
<1 |
|
SSM |
4 |
6 |
2-4 |
Sec |
|
Top |
4 |
7 |
2Š4 |
7-60 |
|
Tops |
6 |
7 |
1Š3 |
< 5 |
|
Tops |
2 |
7 |
1Š7 |
<1 |
|
Vast |
2 |
7 |
1Š7 |
4-8 |
There are some other highly probable members of this family (all of them
have higher SSAP score than 70 ) including: 1bht, 1nk1, 2hpp and 2spt . All of
them found even with classical Blast at CMBI
.
1bht,1nk1 and 2spt were already added to the kringle domain fold in the
latest version of the CATH.