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Status: Done started: 2019-Dec-12 00:35:53 UTC
Project Name1wr4
SequenceGSPGLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIM
Secondary structure

CCCCCCCCEEEEECCCCCEEEEECCCCEEECCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2019-Dec-12 06:55 UTC

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

Cluster #123456789
Cluster density23.319.57.86.43.12.72.61.41.0
Cluster size10895524020171585
Average cluster RMSD4.64.96.66.36.56.45.85.94.9

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 6.69 9.97 12.50 11.50 13.40 14.60 16.70 20.90
2 6.69 0.00 7.97 12.40 9.83 12.10 13.40 16.70 17.90
3 9.97 7.97 0.00 6.92 8.61 10.80 9.31 13.80 16.70
4 12.50 12.40 6.92 0.00 10.50 12.80 8.34 12.50 17.50
5 11.50 9.83 8.61 10.50 0.00 7.90 10.40 10.60 15.10
6 13.40 12.10 10.80 12.80 7.90 0.00 9.64 9.08 11.80
7 14.60 13.40 9.31 8.34 10.40 9.64 0.00 9.26 11.70
8 16.70 16.70 13.80 12.50 10.60 9.08 9.26 0.00 10.10
9 20.90 17.90 16.70 17.50 15.10 11.80 11.70 10.10 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 0.52 0.41 0.30 0.29 0.29 0.34 0.30 0.29
2 0.52 1.00 0.42 0.36 0.34 0.34 0.30 0.29 0.29
3 0.41 0.42 1.00 0.42 0.34 0.33 0.34 0.35 0.28
4 0.30 0.36 0.42 1.00 0.37 0.28 0.30 0.31 0.31
5 0.29 0.34 0.34 0.37 1.00 0.33 0.32 0.32 0.31
6 0.29 0.34 0.33 0.28 0.33 1.00 0.30 0.30 0.31
7 0.34 0.30 0.34 0.30 0.32 0.30 1.00 0.30 0.32
8 0.30 0.29 0.35 0.31 0.32 0.30 0.30 1.00 0.42
9 0.29 0.29 0.28 0.31 0.31 0.31 0.32 0.42 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