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Table 1 Summary of the benchmark results.

From: Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach

NAMEa

PDBb

Res.c (Å)

ORDERd

PATHe

Pred. Structuresf

Cα-RMSDi

BtuCD

1L7V

3.2

Dimer

a

A-Bs1678 g

0.63

BRD*

1BRR

2.9

Trimer

b

A-Bs162-Cs14

1.04

AmtB

1U77

1.35

Trimer

a

A-Bs7-Cs1

1.17

    

b

A-Bs7-Cs1

0.83

    

c

A-Bs1-Cs1

0.75

AcrB

1IWG

3.5

Trimer

a

A-Bs4-Cs1

2.78

    

b

A-Bs4-Cs1

1.56

    

c

A-Bs1-Cs1

1.64

KcsA*

1BL8

3.3

Tetramer

a

A-Bs1-Cs500-Ds2 h

1.79

    

b

A-Bs1-Cs1-Ds2

2.45

    

c

A-Bs2-Cs1-Ds2

2.77

AQP1

1J4N

2.2

Tetramer

a

A-Bs2-Cs1-Ds1

1.31

    

b

A-Bs1-Cs2-Ds1

1.71

    

c

A-Bs2-Cs4-Ds1

1.37

GlpF

1FX8

2.2

Tetramer

a

A-Bs2-Cs1-Ds1

1.11

    

b

A-Bs1-Cs2-Ds1

1.16

    

c

A-Bs2-Cs2-Ds1

1.39

KirBac1

1P7B

3.65

Tetramer

a

A-Bs3-Cs1-Ds1

1.53

    

b

A-Bs3-Cs1-Ds3

1.47

    

c

A-Bs2-Cs1-Ds1

1.80

MscL*

1MSL

3.5

Pentamer

a

A-Bs5-Cs1-Ds4-Es6

3.45

    

b

A-Bs5-Cs3-Ds2-Es1

2.83

    

c

A-Bs8-Cs1-Ds1-Es6

2.47

MscS*

1MXM

3.9

Eptamer

a

A-Bs3-Cs3-Ds3-Es1-Fs1-Gs1

2.21

    

b

A-Bs3-Cs3-Ds1-Es165-Fs3-Gs1

11.30

    

c

A-Bs3-Cs1-Ds1-Es6-Fs1-Gs1

2.06

  1. aAbbreviated name of the membrane proteins subjected to the benchmarks. Asterisks indicate the systems, for which the asymmetric crystallographic unit contains the biological unit.
  2. bPDB code of the membrane proteins subjected to the benchmarks.
  3. cAtomic resolution (Å) of the crystallographic structures.
  4. dOligomeric order of the biological units. eProbed growing paths (see the text and Figures 6-9 for a detailed explanation). For each protein system, the path that produced the best oligomer, in terms of Cα-RMSD from the native assembly, is highlighted in bold.
  5. fPredicted oligomers: the upper case letter indicates the subunit, whereas the letter "s" followed by a number indicates the solution number in the ZDOCK output list. The best oligomer, in terms of Cα-RMSD from the native assembly, is highlighted in bold.
  6. gThe predicted BtuCD dimer was achieved following a dipole-moment-based approach for A subunit reorientation. The same path, but using a membrane topology-based approach for A subunit reorientation, led to the A-Bs1584 dimer characterized by a Cα-RMSD of 0.48 Å from the native dimer.
  7. hThe best predicted KcsA tetramer was achieved following a dipole-moment-based approach for A subunit reorientation. The same path, but using a membrane topology-based approach for A subunit reorientation, led to the A-Bs2-Cs12-Ds4 tetramer characterized by a Cα-RMSD of 0.94 Å from the native oligomer.
  8. iCα-RMSD (Å) between the native and the predicted oligomer from each growing path. For each system, the lowest Cα-RMSD is highlighted in bold.
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BMC Bioinformatics

ISSN: 1471-2105

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