Welcome to the Utrecht Biomolecular Interaction Web Portal >>

HADDOCK server status for job "AcrB-rifampicin-surface"


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 A.M.J.J. Bonvin (2016). "The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes."
J. Mol. Biol., 428, 720-725 (2015).

and add the following acknowledgment:

The FP7 WeNMR (project# 261572), H2020 West-Life (project# 675858) and the EOSC-hub (project# 777536) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid.

How would you rate your experience with our portal? sentiment_very_dissatisfied sentiment_dissatisfied sentiment_neutral sentiment_satisfied sentiment_very_satisfied

Questions / feedback ? ask.bioexcel.eu

Announcing the 2020 EMBO practical course on Integrative Modelling of Biomolecular Interactions.
It will take place at the Izmir Biomedicine and Genome Center (IBG), May 30 - June 5, 2021.

In the aim to improve our new web portal, we would really appreciate 2 min of your time to complete a short survey here! Thanks!

Post-processing: SUCCESS

Summary

HADDOCK clustered 391 structures in 12 cluster(s), which represents 97 % 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.

You can also download all cluster files (best 4 of the top 10 cluster(s)).


Cluster 1

HADDOCK score -42.7 +/- 3.9
Cluster size 64
RMSD from the overall lowest-energy structure 0.6 +/- 0.4
Van der Waals energy -31.1 +/- 4.8
Electrostatic energy -19.5 +/- 18.1
Desolvation energy -9.6 +/- 10.2
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 806.3 +/- 137.4
Z-Score -1.7

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

Cluster 2

HADDOCK score -41.0 +/- 4.0
Cluster size 58
RMSD from the overall lowest-energy structure 0.7 +/- 0.1
Van der Waals energy -30.8 +/- 5.3
Electrostatic energy -9.2 +/- 16.8
Desolvation energy -9.3 +/- 8.6
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 843.0 +/- 140.1
Z-Score -1.2

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

Cluster 4

HADDOCK score -38.8 +/- 1.9
Cluster size 56
RMSD from the overall lowest-energy structure 1.0 +/- 0.0
Van der Waals energy -34.0 +/- 5.5
Electrostatic energy -9.0 +/- 16.6
Desolvation energy -3.9 +/- 2.8
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 915.2 +/- 43.6
Z-Score -0.5

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

Cluster 6

HADDOCK score -37.5 +/- 2.6
Cluster size 22
RMSD from the overall lowest-energy structure 0.9 +/- 0.2
Van der Waals energy -27.3 +/- 3.6
Electrostatic energy -7.1 +/- 13.6
Desolvation energy -9.5 +/- 4.1
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 849.1 +/- 54.0
Z-Score -0.1

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

Cluster 5

HADDOCK score -37.4 +/- 3.3
Cluster size 36
RMSD from the overall lowest-energy structure 0.9 +/- 0.2
Van der Waals energy -32.0 +/- 1.8
Electrostatic energy -5.3 +/- 7.2
Desolvation energy -4.9 +/- 3.9
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 850.5 +/- 97.5
Z-Score -0.0

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

Cluster 3

HADDOCK score -37.4 +/- 2.5
Cluster size 56
RMSD from the overall lowest-energy structure 0.8 +/- 0.2
Van der Waals energy -34.0 +/- 5.5
Electrostatic energy -8.7 +/- 11.4
Desolvation energy -2.5 +/- 4.3
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 906.6 +/- 72.9
Z-Score -0.0

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

Cluster 10

HADDOCK score -37.0 +/- 5.5
Cluster size 15
RMSD from the overall lowest-energy structure 0.9 +/- 0.2
Van der Waals energy -30.6 +/- 4.6
Electrostatic energy -26.3 +/- 16.8
Desolvation energy -3.8 +/- 2.3
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 842.2 +/- 165.3
Z-Score 0.1

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

Cluster 7

HADDOCK score -36.7 +/- 4.4
Cluster size 21
RMSD from the overall lowest-energy structure 1.1 +/- 0.3
Van der Waals energy -28.4 +/- 3.2
Electrostatic energy -23.5 +/- 21.7
Desolvation energy -5.9 +/- 1.3
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 764.7 +/- 142.0
Z-Score 0.2

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

Cluster 12

HADDOCK score -32.3 +/- 3.6
Cluster size 11
RMSD from the overall lowest-energy structure 1.3 +/- 0.2
Van der Waals energy -24.7 +/- 2.9
Electrostatic energy -18.2 +/- 19.2
Desolvation energy -5.7 +/- 1.6
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 716.7 +/- 36.0
Z-Score 1.6

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

Cluster 9

HADDOCK score -32.1 +/- 0.4
Cluster size 17
RMSD from the overall lowest-energy structure 1.7 +/- 0.1
Van der Waals energy -23.3 +/- 1.8
Electrostatic energy -13.6 +/- 18.3
Desolvation energy -7.4 +/- 2.8
Restraints violation energy 0.0 +/- 0.0
Buried Surface Area 629.4 +/- 121.7
Z-Score 1.7

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

Model Analysis (Download all plots)


Cluster Analysis