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Table 1 The IFACEwat improves both the number of hits and the rank of the first hit for either protein complex cases of with- or without interfacial water.

From: IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking

Crystal structure contains WAT

Complex

Type

↑ number of hits

↑ rank of the first hit

   

ZDOCK

IFACEwat

ZDOCK

IFACEwat

ΔGinterface(1sthit)

No

1FC2

O

16

20

-

-

-

 

4CPA

E

-

-

51

4

-26.14

 

1QA9

O

-

-

2

1

-76.04

 

2AYO

O

-

-

32

10

-47.54

 

2HLE

O

-

-

2

1

-178.17

 

2VDB

O

-

-

57

18

-58.42

 

3BP8

O

-

-

11

3

-32.08

Yes

1DQJ

A

6

7

-

-

-

 

1BGX

A

0

1

-

1

-348.73

 

1K4C

AB

1

3

-

-

-

 

1KXQ

AB

0

1

-

1

-191.97

 

1CLV

E

140

141

-

-

-

 

2O3B

E

-

-

7

5

-47.95

 

1YVB

E

0

1

-

2

-55.84

 

1FLE

E

-

-

6

4

-47.85

 

1AK4

O

0

1

-

3

-44.51

 

1FQJ

O

2

4

-

-

-

 

1H9D

O

0

1

-

1

-131.85

 

1HCF

O

0

1

-

1

-175.53

 

1RV6

O

0

1

-

3

-110.72

 

1T6B

O

3

5

-

-

-

 

1Z0K

O

0

1

-

1

-133.32

 

1Z5Y

O

2

3

-

-

-

 

2A9K

O

0

1

-

2

-161.63

 

2B4J

O

6

8

-

-

-

 

1MQ8

O

4

5

-

-

-

 

1R6Q

O

3

4

-

-

-

 

2CFH

O

9

10

-

-

-

 

2OZA

O

1

2

-

-

-

 

2ZOE

O

6

8

-

-

-

 

2BTF

O

-

-

6

1

-142.31

 

2OOR

O

0

3

-

1

-141.03

  1. "-" represents "not applicable" for the corresponding cases. For examples, in the first case [PDB:1FC2], it is found that IFACEwat improves the number of hits (i.e. 4 hits more than ZDOCK), but does not improve the rank of the first hit (e.g. the first hit found by both IFACEwat and ZDOCK is ranked at top-1). Also noted in this table that ∆Ginterface value is only shown for the first hit of the case, in which the rank of the first hit is improved by the IFACEwat.
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BMC Bioinformatics

ISSN: 1471-2105

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