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Status: Done started: 2016-Mar-30 15:35:35 UTC
Project Nameseq56
SequenceFDFRIESVVCLQDSVLAFWKHGMQGKSFKSDEVTQEISDETRVF
Secondary structure

CCCCEEEEEEECHHHHHHHHHCCCCCCCCCCCCEEECCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Mar-30 23:42 UTC

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

Cluster #123456789
Cluster density29.58.45.04.43.42.42.31.51.3
Cluster size150643528281916119
Average cluster RMSD5.17.67.06.48.27.86.97.36.8

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.

#123456789
1 0.00 9.32 10.50 12.10 8.64 13.10 14.70 14.20 15.40
2 9.32 0.00 8.57 10.30 11.80 12.40 10.30 11.50 13.00
3 10.50 8.57 0.00 11.80 11.90 11.10 8.69 9.82 13.60
4 12.10 10.30 11.80 0.00 11.00 13.00 9.15 12.50 11.20
5 8.64 11.80 11.90 11.00 0.00 12.50 12.40 10.50 10.60
6 13.10 12.40 11.10 13.00 12.50 0.00 10.50 13.00 13.30
7 14.70 10.30 8.69 9.15 12.40 10.50 0.00 10.10 10.60
8 14.20 11.50 9.82 12.50 10.50 13.00 10.10 0.00 10.60
9 15.40 13.00 13.60 11.20 10.60 13.30 10.60 10.60 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.

#123456789
1 1.00 0.46 0.41 0.39 0.45 0.31 0.40 0.31 0.31
2 0.46 1.00 0.43 0.34 0.38 0.31 0.39 0.31 0.34
3 0.41 0.43 1.00 0.33 0.39 0.28 0.44 0.32 0.37
4 0.39 0.34 0.33 1.00 0.36 0.32 0.33 0.33 0.34
5 0.45 0.38 0.39 0.36 1.00 0.32 0.32 0.32 0.32
6 0.31 0.31 0.28 0.32 0.32 1.00 0.36 0.27 0.28
7 0.40 0.39 0.44 0.33 0.32 0.36 1.00 0.31 0.38
8 0.31 0.31 0.32 0.33 0.32 0.27 0.31 1.00 0.35
9 0.31 0.34 0.37 0.34 0.32 0.28 0.38 0.35 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.


 

© Laboratory of Theory of Biopolymers 2013