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Status: Done started: 2020-Mar-29 07:49:59 UTC
Project NameAVP0235
SequenceKKKKVVAPTYVLV
Secondary structure

CCEEEEECEEEEC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Mar-29 12:29 UTC

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

Cluster #12345678
Cluster density112.629.416.813.911.19.78.06.6
Cluster size15962322923231616
Average cluster RMSD1.42.11.92.12.12.42.02.4

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 2.18 2.98 3.19 7.95 3.41 5.99 5.08
2 2.18 0.00 3.13 2.75 8.01 3.30 5.91 5.09
3 2.98 3.13 0.00 4.69 9.43 3.73 7.37 5.71
4 3.19 2.75 4.69 0.00 5.98 3.09 3.86 3.84
5 7.95 8.01 9.43 5.98 0.00 6.77 3.00 4.61
6 3.41 3.30 3.73 3.09 6.77 0.00 4.65 3.48
7 5.99 5.91 7.37 3.86 3.00 4.65 0.00 3.06
8 5.08 5.09 5.71 3.84 4.61 3.48 3.06 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 0.81 0.63 0.65 0.65 0.65 0.65 0.61
2 0.81 1.00 0.63 0.69 0.60 0.69 0.60 0.61
3 0.63 0.63 1.00 0.54 0.50 0.61 0.58 0.52
4 0.65 0.69 0.54 1.00 0.63 0.67 0.71 0.58
5 0.65 0.60 0.50 0.63 1.00 0.61 0.71 0.61
6 0.65 0.69 0.61 0.67 0.61 1.00 0.63 0.65
7 0.65 0.60 0.58 0.71 0.71 0.63 1.00 0.75
8 0.61 0.61 0.52 0.58 0.61 0.65 0.75 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