HADDOCK server status for docking run PRE5-PUP2-MS-crosslinks-interface

Status: FINISHED

Your HADDOCK run has successfully completed. The complete run can be downloaded as a gzipped tar file here. The file containing your docking parameters is here.

Please cite the following paper in your work:
G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and (2016). "The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes."
J. Mol. Biol., 428, 720-725 (2015).

Questions / feedback ? ask.bioexcel.eu

Summary

HADDOCK clustered 142 structures in 11 cluster(s), which represents 71.0 % of the water-refined models HADDOCK generated. Note that currently the maximum number of models considered for clustering is 200.

The statistics of the top 10 clusters are shown below. The top cluster is the most reliable according to HADDOCK. Its Z-score indicates how many standard deviations from the average this cluster is located in terms of score (the more negative the better).

A graphical representation of the results is also provided at the bottom of the page.

Cluster 1

Cluster 3

Cluster 2

Cluster 4

Cluster 8

Cluster 6

Cluster 11

Cluster 7

Cluster 9

Cluster 5

Results analysis: The results and graphics presented below are based on water-refined models generated by HADDOCK. The clusters (indicated in color in the graphs) are calculated based on the interface-ligand RMSDs calculated by HADDOCK, with the interface defined automatically based on all observed contacts. The various structural analysis (FCC, i-RMSD and l-RMSD) are made with respect to the best HADDOCK model (the one with the lowest HADDOCK score).
Supplementary information:: i-RMSD -> interface-RMSD calculated on the backbone (CA,C,N,O,P) atoms of all residues involved in intermolecular contact using a 10Å cutoff
l-RMSD -> ligand-RMSD calculated on the backbone atoms (CA,C,N,O,P) of all (N>1) molecules after fitting on the backbone atoms of the first (N=1) molecule
FCC -> Fraction of common contacts. The intermolecular contacts are defined based on the best HADDOCK model using a 5Å cutoff (see Rodrigues et al, Proteins 2012)
a.u. -> Arbitrary Units
The cluster averages and standard deviations are indicated by colored dots with associated error bars. The average values are calculated on the best 4 structures of each clusters (based on the HADDOCK score).

Note that HADDOCK results are deleted after one week.

HADDOCK score	-120.7 +/- 3.5
Cluster size	55
RMSD from the overall lowest-energy structure	0.5 +/- 0.3
Van der Waals energy	-87.1 +/- 6.8
Electrostatic energy	-199.6 +/- 35.2
Desolvation energy	-22.9 +/- 6.6
Restraints violation energy	292.7 +/- 29.11
Buried Surface Area	2592.5 +/- 62.2
Z-Score	-1.8

Nr 1 best structure	Download structure
Nr 2 best structure	Download structure
Nr 3 best structure	Download structure
Nr 4 best structure	Download structure

HADDOCK score	-106.9 +/- 3.3
Cluster size	12
RMSD from the overall lowest-energy structure	3.0 +/- 0.1
Van der Waals energy	-70.4 +/- 6.6
Electrostatic energy	-321.5 +/- 50.6
Desolvation energy	-2.0 +/- 14.3
Restraints violation energy	298.6 +/- 20.88
Buried Surface Area	2190.1 +/- 70.2
Z-Score	-1.1

Nr 1 best structure	Download structure
Nr 2 best structure	Download structure
Nr 3 best structure	Download structure
Nr 4 best structure	Download structure

HADDOCK score	-101.2 +/- 5.6
Cluster size	27
RMSD from the overall lowest-energy structure	5.3 +/- 0.4
Van der Waals energy	-85.2 +/- 7.7
Electrostatic energy	-200.7 +/- 67.6
Desolvation energy	2.2 +/- 4.6
Restraints violation energy	219.2 +/- 88.26
Buried Surface Area	2639.3 +/- 77.7
Z-Score	-0.8

HADDOCK score	-94.8 +/- 13.3
Cluster size	9
RMSD from the overall lowest-energy structure	3.9 +/- 0.2
Van der Waals energy	-66.2 +/- 5.5
Electrostatic energy	-206.8 +/- 53.6
Desolvation energy	-5.1 +/- 8.8
Restraints violation energy	178.2 +/- 19.21
Buried Surface Area	2535.1 +/- 234.0
Z-Score	-0.4

HADDOCK score	-85.5 +/- 6.9
Cluster size	5
RMSD from the overall lowest-energy structure	2.2 +/- 0.2
Van der Waals energy	-79.5 +/- 3.7
Electrostatic energy	-245.0 +/- 24.9
Desolvation energy	2.8 +/- 5.9
Restraints violation energy	401.9 +/- 69.17
Buried Surface Area	2347.9 +/- 144.9
Z-Score	0.1

HADDOCK score	-82.3 +/- 3.3
Cluster size	8
RMSD from the overall lowest-energy structure	2.4 +/- 0.2
Van der Waals energy	-58.9 +/- 3.2
Electrostatic energy	-227.7 +/- 43.3
Desolvation energy	-2.8 +/- 6.7
Restraints violation energy	249.6 +/- 33.28
Buried Surface Area	2073.7 +/- 72.2
Z-Score	0.3

HADDOCK score	-80.9 +/- 11.6
Cluster size	4
RMSD from the overall lowest-energy structure	5.9 +/- 0.1
Van der Waals energy	-64.2 +/- 4.2
Electrostatic energy	-187.7 +/- 21.8
Desolvation energy	0.6 +/- 8.3
Restraints violation energy	202.1 +/- 56.00
Buried Surface Area	2253.3 +/- 67.2
Z-Score	0.3

HADDOCK score	-78.0 +/- 18.5
Cluster size	5
RMSD from the overall lowest-energy structure	6.1 +/- 0.1
Van der Waals energy	-63.4 +/- 10.2
Electrostatic energy	-216.2 +/- 29.9
Desolvation energy	2.9 +/- 7.6
Restraints violation energy	258.3 +/- 38.82
Buried Surface Area	2245.1 +/- 145.6
Z-Score	0.5

HADDOCK score	-66.8 +/- 1.1
Cluster size	5
RMSD from the overall lowest-energy structure	5.2 +/- 0.3
Van der Waals energy	-50.5 +/- 6.8
Electrostatic energy	-148.4 +/- 29.4
Desolvation energy	-5.7 +/- 8.1
Restraints violation energy	190.3 +/- 52.65
Buried Surface Area	2010.5 +/- 194.7
Z-Score	1.1

HADDOCK score	-54.8 +/- 9.3
Cluster size	8
RMSD from the overall lowest-energy structure	4.4 +/- 0.4
Van der Waals energy	-53.9 +/- 3.5
Electrostatic energy	-166.8 +/- 51.3
Desolvation energy	10.7 +/- 10.7
Restraints violation energy	217.5 +/- 48.68
Buried Surface Area	2108.8 +/- 110.4
Z-Score	1.8