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Status: Done started: 2017-Sep-02 20:20:55 UTC
Project NameCDTM
SequenceGLDFACDIYIWAPLAGTCGVLLLSLVITLYCNHRNRRRVCKCPRPVVKSGDKPSLSARYV
Secondary structure

CCCEEECCCEECCCCCHHHHHHHHHHHHHHEECCCCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Sep-03 04:05 UTC

Time evolution of structural features: CABS energy, End-to-end distance and Radius of gyration.

Cluster #12345678910
Cluster density35.910.34.54.23.52.51.30.90.40.3
Cluster size140793935251911822
Average cluster RMSD3.97.78.88.47.27.68.28.45.65.8

Clustering of protein models is the task of separating a set of protein models (here a protein dynamics trajectory) into groups (called clusters). The clustering is done in such a way that models are more similar in the same group to each other (here in the sense of RMSD measure), than those in other groups (clusters). CABSfold utilizes classical K-means clustering method.
After clustering is done, each cluster representative is chosen (always the model which average dissimilarity to all models in a cluster is minimal). Predicted protein models, presented in the Predicted structures tab, are each cluster representatives (the clusters and the corresponding models are marked by the same numbers, e.g. Model 1 represents Cluster 1).
The clusters are numbered/ranked according to cluster density values, from the most dense (numbered as a first) to the least dense one.

#12345678910
1 0.00 6.89 8.78 9.55 12.90 13.10 15.10 16.40 21.10 21.10
2 6.89 0.00 7.83 8.56 10.50 11.90 11.70 14.30 19.10 18.90
3 8.78 7.83 0.00 10.70 12.40 13.60 11.70 15.60 19.10 18.30
4 9.55 8.56 10.70 0.00 9.47 10.40 11.90 16.50 20.30 16.30
5 12.90 10.50 12.40 9.47 0.00 14.10 9.85 14.70 19.20 15.60
6 13.10 11.90 13.60 10.40 14.10 0.00 12.80 12.80 17.40 16.40
7 15.10 11.70 11.70 11.90 9.85 12.80 0.00 14.90 15.30 12.90
8 16.40 14.30 15.60 16.50 14.70 12.80 14.90 0.00 14.50 18.70
9 21.10 19.10 19.10 20.30 19.20 17.40 15.30 14.50 0.00 19.30
10 21.10 18.90 18.30 16.30 15.60 16.40 12.90 18.70 19.30 0.00

The table contains RMSD values (calculated on the Cα atoms) between the predicted models.
Read more about the root-mean-square deviation (RMSD) measure.

#12345678910
1 1.00 0.45 0.41 0.37 0.35 0.33 0.40 0.37 0.29 0.29
2 0.45 1.00 0.41 0.37 0.37 0.32 0.35 0.36 0.26 0.29
3 0.41 0.41 1.00 0.33 0.34 0.33 0.31 0.36 0.29 0.26
4 0.37 0.37 0.33 1.00 0.34 0.31 0.36 0.32 0.26 0.29
5 0.35 0.37 0.34 0.34 1.00 0.33 0.33 0.31 0.26 0.28
6 0.33 0.32 0.33 0.31 0.33 1.00 0.30 0.29 0.30 0.29
7 0.40 0.35 0.31 0.36 0.33 0.30 1.00 0.29 0.32 0.30
8 0.37 0.36 0.36 0.32 0.31 0.29 0.29 1.00 0.29 0.23
9 0.29 0.26 0.29 0.26 0.26 0.30 0.32 0.29 1.00 0.25
10 0.29 0.29 0.26 0.29 0.28 0.29 0.30 0.23 0.25 1.00

The table contains GDT_TS values (calculated on the Cα atoms) between the predicted models.
Read more about the global distance test (GDT, also written as GDT_TS to represent "total score") measure.


 

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