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Status: Done started: 2020-May-08 19:38:55 UTC
Project Name770
SequenceALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFEL
Secondary structure

CCCCCCCCCCCCEEEEECCCCCCEEEEEEEEEC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-May-09 02:41 UTC

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

Cluster #12345678910
Cluster density82.410.16.46.15.43.93.92.21.70.8
Cluster size1514827392721241274
Average cluster RMSD1.84.74.26.45.05.46.25.54.25.2

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 5.43 3.78 7.15 5.47 9.43 11.00 11.80 10.40 15.70
2 5.43 0.00 5.16 6.24 5.84 7.23 7.41 8.40 9.18 14.70
3 3.78 5.16 0.00 6.38 6.09 9.54 9.81 11.30 10.50 14.50
4 7.15 6.24 6.38 0.00 7.63 7.39 8.11 7.22 10.20 14.90
5 5.47 5.84 6.09 7.63 0.00 6.67 9.80 9.36 7.23 13.40
6 9.43 7.23 9.54 7.39 6.67 0.00 8.86 5.66 5.66 14.30
7 11.00 7.41 9.81 8.11 9.80 8.86 0.00 6.68 12.40 10.10
8 11.80 8.40 11.30 7.22 9.36 5.66 6.68 0.00 8.72 13.20
9 10.40 9.18 10.50 10.20 7.23 5.66 12.40 8.72 0.00 15.20
10 15.70 14.70 14.50 14.90 13.40 14.30 10.10 13.20 15.20 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 0.42 0.55 0.34 0.53 0.33 0.32 0.29 0.46 0.39
2 0.42 1.00 0.52 0.39 0.48 0.45 0.38 0.37 0.38 0.40
3 0.55 0.52 1.00 0.36 0.47 0.34 0.33 0.29 0.42 0.38
4 0.34 0.39 0.36 1.00 0.35 0.38 0.41 0.35 0.33 0.31
5 0.53 0.48 0.47 0.35 1.00 0.39 0.36 0.30 0.45 0.39
6 0.33 0.45 0.34 0.38 0.39 1.00 0.30 0.39 0.40 0.33
7 0.32 0.38 0.33 0.41 0.36 0.30 1.00 0.49 0.31 0.42
8 0.29 0.37 0.29 0.35 0.30 0.39 0.49 1.00 0.36 0.33
9 0.46 0.38 0.42 0.33 0.45 0.40 0.31 0.36 1.00 0.35
10 0.39 0.40 0.38 0.31 0.39 0.33 0.42 0.33 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