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Status: Done started: 2020-Mar-23 14:28:35 UTC
Project NameAVP1877
SequenceINASVVNIQKEIDRLNEVAKNLNESLIDL
Secondary structure

CCHHHHHHHHHHHHHHHHHHHHHHHHHCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Mar-23 18:50 UTC

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

Cluster #12345678910
Cluster density84.655.334.625.216.713.111.35.64.83.0
Cluster size10071473730222312117
Average cluster RMSD1.21.31.41.51.81.72.02.12.32.3

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 0.47 0.66 0.66 1.00 1.17 1.57 1.96 3.31 3.92
2 0.47 0.00 0.75 0.72 0.84 1.21 1.44 1.99 3.37 3.86
3 0.66 0.75 0.00 0.92 1.14 1.42 1.33 2.07 3.39 3.99
4 0.66 0.72 0.92 0.00 1.12 1.19 1.53 2.30 3.47 4.28
5 1.00 0.84 1.14 1.12 0.00 1.01 1.41 2.16 3.53 4.02
6 1.17 1.21 1.42 1.19 1.01 0.00 1.51 2.26 3.38 4.22
7 1.57 1.44 1.33 1.53 1.41 1.51 0.00 2.33 3.50 4.18
8 1.96 1.99 2.07 2.30 2.16 2.26 2.33 0.00 3.05 3.19
9 3.31 3.37 3.39 3.47 3.53 3.38 3.50 3.05 0.00 3.50
10 3.92 3.86 3.99 4.28 4.02 4.22 4.18 3.19 3.50 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 0.99 0.98 0.98 0.97 0.95 0.91 0.91 0.66 0.77
2 0.99 1.00 0.97 0.98 0.97 0.94 0.92 0.91 0.66 0.78
3 0.98 0.97 1.00 0.96 0.96 0.94 0.93 0.90 0.66 0.78
4 0.98 0.98 0.96 1.00 0.96 0.95 0.93 0.91 0.66 0.76
5 0.97 0.97 0.96 0.96 1.00 0.97 0.93 0.91 0.66 0.78
6 0.95 0.94 0.94 0.95 0.97 1.00 0.93 0.91 0.67 0.76
7 0.91 0.92 0.93 0.93 0.93 0.93 1.00 0.88 0.66 0.76
8 0.91 0.91 0.90 0.91 0.91 0.91 0.88 1.00 0.66 0.78
9 0.66 0.66 0.66 0.66 0.66 0.67 0.66 0.66 1.00 0.63
10 0.77 0.78 0.78 0.76 0.78 0.76 0.76 0.78 0.63 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