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Status: Done started: 2019-Dec-18 18:44:33 UTC
Project Name1pv0_r2
SequenceMRKLSDELLIESYFKATEMNLNRDFIELIENEIKRRSLGHIISVSS
Secondary structure

CCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCC

Simulation (CABS) temperature2.5 - 1.0
Estimated finish time2019-Dec-19 01:28 UTC

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

Cluster #123456789
Cluster density35.021.317.116.715.88.05.23.70.8
Cluster size4783424972253174
Average cluster RMSD1.33.92.52.94.63.16.01.94.8

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 8.65 2.76 4.24 7.41 5.65 9.12 17.30 13.00
2 8.65 0.00 7.74 7.66 4.89 8.45 3.32 16.60 12.40
3 2.76 7.74 0.00 4.57 6.29 5.62 8.21 17.00 12.50
4 4.24 7.66 4.57 0.00 8.05 3.15 8.49 16.10 12.50
5 7.41 4.89 6.29 8.05 0.00 9.10 4.21 16.70 11.40
6 5.65 8.45 5.62 3.15 9.10 0.00 9.43 15.10 12.20
7 9.12 3.32 8.21 8.49 4.21 9.43 0.00 16.50 11.80
8 17.30 16.60 17.00 16.10 16.70 15.10 16.50 0.00 8.91
9 13.00 12.40 12.50 12.50 11.40 12.20 11.80 8.91 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 0.48 0.72 0.57 0.54 0.51 0.47 0.50 0.33
2 0.48 1.00 0.52 0.58 0.59 0.66 0.61 0.39 0.32
3 0.72 0.52 1.00 0.61 0.55 0.57 0.49 0.45 0.32
4 0.57 0.58 0.61 1.00 0.61 0.68 0.56 0.51 0.29
5 0.54 0.59 0.55 0.61 1.00 0.61 0.68 0.44 0.35
6 0.51 0.66 0.57 0.68 0.61 1.00 0.54 0.46 0.33
7 0.47 0.61 0.49 0.56 0.68 0.54 1.00 0.39 0.34
8 0.50 0.39 0.45 0.51 0.44 0.46 0.39 1.00 0.42
9 0.33 0.32 0.32 0.29 0.35 0.33 0.34 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