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Status: Done started: 2018-Mar-22 14:32:41 UTC
Project NameBB2ndTryDTW
SequenceSSDSIGVLGYQKTVDHTKVNSKLSLF
Secondary structure

CCCEEEEEEEEEEEEEEEECCEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2018-Mar-22 19:25 UTC

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

Cluster #12345678
Cluster density33.124.411.911.210.39.35.03.8
Cluster size8364494142382122
Average cluster RMSD2.52.64.13.74.14.14.25.7

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.

#12345678
1 0.00 3.88 14.30 15.80 4.37 11.10 15.40 10.20
2 3.88 0.00 16.60 17.90 6.20 13.10 16.70 9.43
3 14.30 16.60 0.00 3.96 13.10 6.33 7.18 13.40
4 15.80 17.90 3.96 0.00 14.20 6.77 6.76 13.90
5 4.37 6.20 13.10 14.20 0.00 8.92 14.50 10.30
6 11.10 13.10 6.33 6.77 8.92 0.00 7.77 10.10
7 15.40 16.70 7.18 6.76 14.50 7.77 0.00 10.60
8 10.20 9.43 13.40 13.90 10.30 10.10 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.

#12345678
1 1.00 0.60 0.44 0.46 0.56 0.42 0.35 0.33
2 0.60 1.00 0.41 0.42 0.46 0.39 0.35 0.36
3 0.44 0.41 1.00 0.57 0.44 0.45 0.49 0.45
4 0.46 0.42 0.57 1.00 0.47 0.49 0.45 0.40
5 0.56 0.46 0.44 0.47 1.00 0.57 0.41 0.38
6 0.42 0.39 0.45 0.49 0.57 1.00 0.50 0.41
7 0.35 0.35 0.49 0.45 0.41 0.50 1.00 0.38
8 0.33 0.36 0.45 0.40 0.38 0.41 0.38 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