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Status: Done started: 2020-Mar-26 21:16:45 UTC
Project NameAVP0047
SequenceTGAWIEFGCHRNKSNLHTEA
Secondary structure

CCCEEEEEEECCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Mar-27 01:38 UTC

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

Cluster #123456789
Cluster density41.530.614.911.78.67.65.74.74.2
Cluster size996651422726181615
Average cluster RMSD2.42.23.43.63.13.43.23.43.6

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 3.71 6.91 5.39 9.68 8.07 11.80 14.50 11.60
2 3.71 0.00 5.24 4.78 7.28 7.23 10.10 13.70 10.70
3 6.91 5.24 0.00 3.96 3.95 3.79 6.06 9.46 6.80
4 5.39 4.78 3.96 0.00 6.26 5.09 7.64 10.70 7.45
5 9.68 7.28 3.95 6.26 0.00 5.07 4.91 8.19 6.17
6 8.07 7.23 3.79 5.09 5.07 0.00 5.47 7.65 6.56
7 11.80 10.10 6.06 7.64 4.91 5.47 0.00 5.68 4.77
8 14.50 13.70 9.46 10.70 8.19 7.65 5.68 0.00 5.62
9 11.60 10.70 6.80 7.45 6.17 6.56 4.77 5.62 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.

#123456789
1 1.00 0.60 0.44 0.51 0.44 0.49 0.45 0.44 0.41
2 0.60 1.00 0.51 0.57 0.46 0.54 0.47 0.44 0.44
3 0.44 0.51 1.00 0.59 0.55 0.60 0.51 0.45 0.54
4 0.51 0.57 0.59 1.00 0.44 0.54 0.46 0.46 0.44
5 0.44 0.46 0.55 0.44 1.00 0.54 0.60 0.50 0.50
6 0.49 0.54 0.60 0.54 0.54 1.00 0.47 0.46 0.45
7 0.45 0.47 0.51 0.46 0.60 0.47 1.00 0.50 0.56
8 0.44 0.44 0.45 0.46 0.50 0.46 0.50 1.00 0.50
9 0.41 0.44 0.54 0.44 0.50 0.45 0.56 0.50 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