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Table 3 Statistics of docking calculations

From: MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry

Docking statistics of Rpn13-Ubiquitin

Parameter

BLa

LP/MS

LP(all)b

CSP-50

CSP-0

CPORT

Random excl.

yes, 50

no

no

yes,50

no

yes, 87.5

No. of clusters

4

9

7

9

2

25

Best cluster c

1

1

2

4

1

5

No. of structures

333

141

79

11

258

13

iRMSD to 2Z59 d

11.24

2.85

11.51

6.70

10.13

7.99

lRMSD to 2Z59 e

21.19

7.76

19.97

13.52

19.11

16.63

fnat f

0.044

0.124

0.012

0.018

0.053

0.003

HADDOCK score g

-78.6

-65.8

-77.5

-72.0

-71.2

-75.4

Best cluster to 2Z59 h

3(2)

1(1)

4(2)

3(2)

2(2)

9(4)

No. of structures

45

141

95

116

141

14

Best iRMSD to 2Z59 i

2.77

2.71

2.66

2.86

1.80

5.00

Average iRMSD to 2Z59

3.79

2.85

3.06

3.23

3.41

5.08

Best lRMSD to 2Z59

6.56

6.42

6.67

7.85

7.99

9.65

Average lRMSD to 2Z59

8.60

7.76

7.07

8.63

9.71

11.12

Best fnat

0.276

0.155

0.147

0.232

0.351

0.008

Average fnat

0.153

0.124

0.090

0.182

0.237

0.003

HADDOCK score

-52.8

-65.8

-60.4

-63.2

-58.3

-40.6

  1. a: BL is a baseline run, where all contacts from the reference structure 2Z59 were included as active residues.
  2. b: LP(all) is similar to the LP/MS run, but not using CPORT prediction for ubiquitin, but instead all 76 ubiquitin residues as passive residues.
  3. c: The cluster with the lowest average HADDOCK score. The number refers to the rank in cluster size.
  4. d: iRMSD is the interface RMSD (within 10 Å of the interface), between the average structure in the cluster and the lowest energy structure of the reference [PDB:2Z59].
  5. e: lRMSD is the ligand RMSD (the average structure and lowest energy structure of the reference ensemble [PDB:2Z59] are fitted on the backbone atoms of the larger protein, Rpn13, and the RMSD is calculated for the smaller, ubiquitin), between the average structure in the cluster and the reference [PDB:2Z59].
  6. f: The fraction of native contacts is calculated by counting all contacts (residue-wise) between Rpn13 and ubiquitin in the reference structure and comparing how many are retrieved for the average structure in each cluster.
  7. g: The average HADDOCK score of the four lowest energy structures in the cluster (in kcal/mol).
  8. h: Deemed by the lowest iRMSD compared with [PDB:2Z59] of the four lowest energy structures in the cluster. The first number is the rank in HADDOCK score, and the second number in parentheses is the rank in cluster size.
  9. i: The “Best” values are the comparison between the one best structure in each cluster and the reference, whereas the “Average” values are averaged over the ten lowest energy structures of each cluster.
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BMC Structural Biology

ISSN: 1472-6807

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