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Status: Done started: 2020-Apr-01 13:07:29 UTC
Project NameAVP0676
SequenceCCFLNITNSHVSILQERPPLENRVLTGWGL
Secondary structure

CEEEEEECCCEEEEEECCCCCCEEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-01 19:30 UTC

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

Cluster #12345678910
Cluster density41.528.520.85.95.53.73.12.00.90.6
Cluster size1017079332518181042
Average cluster RMSD2.42.53.85.64.54.95.95.14.33.5

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 4.29 4.37 7.32 6.46 11.50 9.40 10.70 17.00 17.90
2 4.29 0.00 2.76 5.83 6.73 11.00 11.30 12.80 17.60 18.50
3 4.37 2.76 0.00 5.32 5.49 10.20 11.10 12.40 17.20 18.20
4 7.32 5.83 5.32 0.00 6.62 8.59 10.80 12.30 16.20 16.40
5 6.46 6.73 5.49 6.62 0.00 7.12 10.10 10.40 13.20 14.70
6 11.50 11.00 10.20 8.59 7.12 0.00 12.80 12.40 9.43 11.20
7 9.40 11.30 11.10 10.80 10.10 12.80 0.00 5.29 16.60 12.70
8 10.70 12.80 12.40 12.30 10.40 12.40 5.29 0.00 14.80 11.10
9 17.00 17.60 17.20 16.20 13.20 9.43 16.60 14.80 0.00 9.62
10 17.90 18.50 18.20 16.40 14.70 11.20 12.70 11.10 9.62 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 0.65 0.62 0.38 0.46 0.42 0.38 0.41 0.42 0.30
2 0.65 1.00 0.72 0.46 0.47 0.44 0.41 0.39 0.38 0.34
3 0.62 0.72 1.00 0.47 0.55 0.47 0.44 0.43 0.39 0.33
4 0.38 0.46 0.47 1.00 0.37 0.39 0.38 0.35 0.38 0.34
5 0.46 0.47 0.55 0.37 1.00 0.49 0.34 0.47 0.39 0.34
6 0.42 0.44 0.47 0.39 0.49 1.00 0.36 0.35 0.38 0.41
7 0.38 0.41 0.44 0.38 0.34 0.36 1.00 0.47 0.35 0.45
8 0.41 0.39 0.43 0.35 0.47 0.35 0.47 1.00 0.35 0.39
9 0.42 0.38 0.39 0.38 0.39 0.38 0.35 0.35 1.00 0.42
10 0.30 0.34 0.33 0.34 0.34 0.41 0.45 0.39 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