NMR case


Tested structure:

DNA binding domain of rat glucocorticoid receptor Ð 72 amino acids, 38 % SSE
1gdc is an averaged NMR model, 2gda contains 24 models Ð model 11 is most similar to the others, models
2 and 19 are most divergent from the others

Number in parentheses in columnÓ Another true positivesÓ means number of retrieved true positives,

Processing times are in minutes.

 

CE

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

yes

Yes (23)

no

4

2gda 2

yes

Yes (23)

no

7

2gda 7

yes

Yes (23)

no

7

2gda 11

yes

Yes (23)

no

6

2gda 18

yes

Yes (23)

no

10

2gda 19

yes

Yes (23)

no

16

 

Dali

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

no

Yes (1)

no

3

2gda 2

no

Yes (1)

2

ND

2gda 7

no

Yes (1)

no

ND

2gda 11

no

Yes (1)

2

2

2gda 18

no

Yes (1)

no

1

2gda 19

no

Yes (1)

no

2




 

Dejavu

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

no

no

1

69

2gda 2

no

Yes(1)

2

88

2gda 7

no

no

1

88

2gda 11

no

no

1

79

2gda 18

no

no

1

74

2gda 19

no

no

1

78

 

Lock

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

no

Yes(1)

2

4

2gda 2

no

Yes(1)

2

5

2gda 7

no

Yes(1)

2

6

2gda 11

no

Yes(1)

2

4

2gda 18

no

Yes(1)

2

ND

2gda 19

no

Yes(1)

2

6

 

Matras

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

no

Yes(2)

2

3

2gda 2

no

Yes(1)

2

4

2gda 7

no

Yes(1)

2

5

2gda 11

no

Yes (3)

 

4

2gda 18

no

Yes(1)

2

4

2gda 19

no

Yes(1)

2

5

 

Top

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

No

Yes (7)

8

6

2gda 2

No

Yes (7)

8

29

2gda 7

No

Yes (7)

8

19

2gda 11

No

Yes (7)

8

36

2gda 18

No

Yes (7)

8

12

2gda 19

No

Yes (7)

8

15

 

Tops

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

no

Yes(7)

1

1

2gda 2

no

Yes(7)

1

2

2gda 7

 

 

 

 

2gda 11

no

Yes(7)

1

1

2gda 18

no

Yes(7)

1

1

2gda 19

 

 

 

 

 

Topscan

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

no

Yes(7)

1

Sec

2gda 2

no

no

1

Sec

2gda 7

no

no

1

Sec

2gda 11

no

Yes(7)

6

Sec

2gda 18

no

Yes(7)

2

Sec

2gda 19

no

no

1

Sec

 

Vast

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

no

Yes(4)

2

5

2gda 2

no

Yes(1)

2

Less than 6

2gda 7

no

Yes(1)

2

Less than 5

2gda 11

no

Yes(1)

2

3

2gda 18

no

Yes(1)

2

5

2gda 19

no

Yes(4)

2

Less than 27

 

 

SSM

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

yes

Yes (8)

No

Sec

2gda 2

yes

Yes(2)

No

Sec

2gda 7

yes

Yes(2)

No

Sec

2gda 11

yes

Yes(2)

No

Sec

2gda 18

ND

 

 

 

2gda 19

yes

Yes(2)

No

Sec

The program couldnÕt detect the SSE in the model 18

 

Pride

Structure/model

Found itself

Found another TP

First FP

Time

1gdc

No

Yes (4)

6

Sec

2gda 2

No

Yes (4)

5

Sec

2gda 7

Yes

Yes (4)

5

Sec

2gda 11

No

Yes (4)

5

Sec

2gda 18

Yes

Yes (4)

6

Sec

2gda 19

No

Yes (4)

5

Sec

 

 

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